Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
PAX2	5076	broad.mit.edu	37	10	102584414	102584414	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102584414T>A	uc001krk.3	+	c.998T>A	c.(997-999)ATG>AAG	p.M333K	PAX2_uc001krl.3_Missense_Mutation_p.M310K|PAX2_uc001krm.3_Missense_Mutation_p.M333K|PAX2_uc001kro.3_Missense_Mutation_p.M310K|PAX2_uc001krn.3_Missense_Mutation_p.M310K|PAX2_uc010qps.1_Missense_Mutation_p.M309K|PAX2_uc001krp.1_Missense_Mutation_p.M306K	NM_003990	NP_003981	Q02962	PAX2_HUMAN	paired box protein 2 isoform e	333					anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve formation|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter development|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|promoter binding|superoxide-generating NADPH oxidase activity|transcription activator activity|transcription repressor activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)										0.144737	57.874752	85.52314	33	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102584414	102584414	11899	10	T	A	A	A	663	51	PAX2	3	3
GRK5	2869	broad.mit.edu	37	10	121212201	121212201	+	Nonsense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:121212201A>T	uc001led.2	+	c.1423A>T	c.(1423-1425)AAG>TAG	p.K475*	GRK5_uc009xzh.2_Nonsense_Mutation_p.K340*	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	475	AGC-kinase C-terminal.				G-protein signaling, coupled to cAMP nucleotide second messenger|protein phosphorylation|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)	2		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)						989				0.128713	13.138116	26.681181	13	88	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	121212201	121212201	7071	10	A	T	T	T	169	13	GRK5	5	3
DHTKD1	55526	broad.mit.edu	37	10	12136268	12136268	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:12136268C>G	uc001ild.3	+	c.1356C>G	c.(1354-1356)ATC>ATG	p.I452M		NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain	452					glycolysis|oxidation-reduction process	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)											0.09375	8.696314	24.625455	9	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12136268	12136268	4679	10	C	G	G	G	369	29	DHTKD1	3	3
DHX32	55760	broad.mit.edu	37	10	127569217	127569217	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:127569217T>A	uc001ljf.1	-	c.177A>T	c.(175-177)AGA>AGT	p.R59S	DHX32_uc001ljg.1_Missense_Mutation_p.R59S	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32	59						mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)												0.14094	26.167053	44.718756	21	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127569217	127569217	4684	10	T	A	A	A	699	54	DHX32	3	3
FANK1	92565	broad.mit.edu	37	10	127685120	127685120	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:127685120C>T	uc009yan.2	+	c.478C>T	c.(478-480)CGT>TGT	p.R160C	FANK1_uc001ljh.3_Missense_Mutation_p.R134C|FANK1_uc001lji.2_Missense_Mutation_p.R128C	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains	134	ANK 1.					cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)												0.139683	71.296768	110.793782	44	271	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127685120	127685120	5908	10	C	T	T	T	299	23	FANK1	1	1
C10orf90	118611	broad.mit.edu	37	10	128118409	128118409	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:128118409G>C	uc010qum.1	-	c.2199C>G	c.(2197-2199)TTC>TTG	p.F733L	C10orf90_uc001ljp.2_Missense_Mutation_p.F492L|C10orf90_uc001ljq.2_Missense_Mutation_p.F636L|C10orf90_uc001ljo.2_Non-coding_Transcript	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611	636											0		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)										0.145161	44.26294	59.282462	18	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128118409	128118409	1660	10	G	C	C	C	581	45	C10orf90	3	3
KNDC1	85442	broad.mit.edu	37	10	135024994	135024994	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:135024994G>T	uc001llz.1	+	c.3977G>T	c.(3976-3978)TGG>TTG	p.W1326L		NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	1326	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					ovary(1)	1		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)										0.1875	44.61778	56.33248	24	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135024994	135024994	8740	10	G	T	T	T	611	47	KNDC1	2	2
FAM171A1	221061	broad.mit.edu	37	10	15325952	15325952	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15325952T>A	uc001iob.2	-	c.250A>T	c.(250-252)AGT>TGT	p.S84C		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	84	Extracellular (Potential).					integral to membrane				ovary(2)|breast(1)	3														0.111111	16.093034	38.947157	17	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15325952	15325952	5695	10	T	A	A	A	715	55	FAM171A1	3	3
ITGA8	8516	broad.mit.edu	37	10	15688991	15688991	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15688991G>T	uc001ioc.1	-	c.1061C>A	c.(1060-1062)CCC>CAC	p.P354H	ITGA8_uc010qcb.1_Missense_Mutation_p.P339H	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	354	Extracellular (Potential).|FG-GAP 5.				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6														0.164179	36.245751	50.536624	22	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15688991	15688991	8186	10	G	T	T	T	559	43	ITGA8	2	2
ANKRD26	22852	broad.mit.edu	37	10	27355419	27355419	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27355419A>G	uc009xku.1	-	c.1266T>C	c.(1264-1266)TCT>TCC	p.S422S	ANKRD26_uc001itg.2_Silent_p.S141S|ANKRD26_uc001ith.2_Silent_p.S422S	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	422										large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4														0.217391	47.154384	53.927694	20	72	KEEP	---	---	---	---	capture		Silent	SNP	27355419	27355419	659	10	A	G	G	G	80	7	ANKRD26	4	4
PCDH15	65217	broad.mit.edu	37	10	55721653	55721653	+	Splice_Site_SNP	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55721653C>T	uc010qhy.1	-	c.2884_splice	c.e23-1	p.G962_splice	PCDH15_uc010qhq.1_Splice_Site_SNP_p.G962_splice|PCDH15_uc010qhr.1_Splice_Site_SNP_p.G957_splice|PCDH15_uc010qhs.1_Splice_Site_SNP_p.G969_splice|PCDH15_uc010qht.1_Splice_Site_SNP_p.G964_splice|PCDH15_uc010qhu.1_Splice_Site_SNP_p.G957_splice|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Splice_Site_SNP_p.G957_splice|PCDH15_uc010qhw.1_Splice_Site_SNP_p.G920_splice|PCDH15_uc010qhx.1_Splice_Site_SNP_p.G886_splice|PCDH15_uc010qhz.1_Splice_Site_SNP_p.G957_splice|PCDH15_uc010qia.1_Splice_Site_SNP_p.G935_splice|PCDH15_uc001jju.1_Splice_Site_SNP_p.G957_splice|PCDH15_uc010qib.1_Splice_Site_SNP_p.G935_splice	NM_001142763	NP_001136235			protocadherin 15 isoform CD1-1 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.147826	32.89772	46.592031	17	98	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	55721653	55721653	11931	10	C	T	T	T	312	24	PCDH15	5	2
RUFY2	55680	broad.mit.edu	37	10	70156631	70156631	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70156631G>T	uc001job.2	-	c.409C>A	c.(409-411)CTG>ATG	p.L137M	RUFY2_uc001jnz.1_Non-coding_Transcript|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Missense_Mutation_p.L44M|RUFY2_uc001jod.1_Missense_Mutation_p.L102M|RUFY2_uc009xpv.1_De_novo_Start_InFrame|RUFY2_uc001joe.1_Missense_Mutation_p.L102M	NM_017987	NP_060457	Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain-containing 2 isoform a	151	RUN.					nucleus	zinc ion binding			ovary(1)	1														0.097561	1.531886	14.846071	8	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70156631	70156631	14219	10	G	T	T	T	425	33	RUFY2	2	2
STOX1	219736	broad.mit.edu	37	10	70645915	70645915	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70645915G>T	uc001jos.2	+	c.2363G>T	c.(2362-2364)AGG>ATG	p.R788M	STOX1_uc001jor.2_Intron|STOX1_uc009xpy.2_Intron|STOX1_uc001joq.2_Missense_Mutation_p.R678M	NM_001130161	NP_001123633	Q6ZVD7	STOX1_HUMAN	storkhead box 1 isoform a	788						cytoplasm|nucleolus	DNA binding			kidney(1)	1														0.121739	12.665167	28.794969	14	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70645915	70645915	15839	10	G	T	T	T	455	35	STOX1	2	2
MAT1A	4143	broad.mit.edu	37	10	82043734	82043734	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:82043734A>T	uc001kbw.2	-	c.230T>A	c.(229-231)GTG>GAG	p.V77E		NM_000429	NP_000420	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	77					cellular amino acid metabolic process|methylation|xenobiotic metabolic process	cytosol	ATP binding|metal ion binding|methionine adenosyltransferase activity				0			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)									0.091743	2.985199	21.29274	10	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82043734	82043734	9713	10	A	T	T	T	78	6	MAT1A	3	3
DYDC2	84332	broad.mit.edu	37	10	82122230	82122230	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:82122230G>T	uc001kca.1	+	c.31G>T	c.(31-33)GGA>TGA	p.G11*	DYDC2_uc001kbz.1_Non-coding_Transcript|DYDC2_uc001kcb.1_Nonsense_Mutation_p.G11*	NM_032372	NP_115748	Q96IM9	DYDC2_HUMAN	DPY30 domain containing 2	11							protein binding				0			Colorectal(32;0.229)											0.188034	38.443004	49.161068	22	95	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	82122230	82122230	5025	10	G	T	T	T	611	47	DYDC2	5	2
TLL2	7093	broad.mit.edu	37	10	98146809	98146809	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98146809G>T	uc001kml.1	-	c.1753C>A	c.(1753-1755)CAC>AAC	p.H585N		NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	585	EGF-like 1; calcium-binding (Potential).			EVDECSWPDHGGCEHRCV -> GKKKKKKKKKKKKKKKKK (in Ref. 5; AAH13871).	cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)										0.08871	1.325393	22.529758	11	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98146809	98146809	16476	10	G	T	T	T	585	45	TLL2	2	2
MMP20	9313	broad.mit.edu	37	11	102464323	102464323	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102464323G>T	uc001phc.2	-	c.1094C>A	c.(1093-1095)CCC>CAC	p.P365H		NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein	365	Hemopexin-like 2.				proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)						637				0.13913	20.01537	34.497141	16	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102464323	102464323	10049	11	G	T	T	T	559	43	MMP20	2	2
CASP4	837	broad.mit.edu	37	11	104819384	104819384	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:104819384C>A	uc001pid.1	-	c.801G>T	c.(799-801)TGG>TGT	p.W267C	CASP4_uc001pib.1_Missense_Mutation_p.W211C|CASP4_uc009yxg.1_Missense_Mutation_p.W176C	NM_001225	NP_001216	P49662	CASP4_HUMAN	caspase 4 isoform alpha precursor	267					apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)						204				0.129412	13.271704	24.633771	11	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104819384	104819384	2792	11	C	A	A	A	286	22	CASP4	2	2
CASP4	837	broad.mit.edu	37	11	104825538	104825538	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:104825538A>G	uc001pid.1	-	c.198T>C	c.(196-198)CGT>CGC	p.R66R	CASP4_uc001pib.1_Silent_p.R10R|CASP4_uc009yxg.1_5'UTR|CASP4_uc010rux.1_Silent_p.R66R|CASP4_uc010ruy.1_Silent_p.R66R	NM_001225	NP_001216	P49662	CASP4_HUMAN	caspase 4 isoform alpha precursor	66	CARD.				apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)						204				0.168269	91.016128	112.675511	35	173	KEEP	---	---	---	---	capture		Silent	SNP	104825538	104825538	2792	11	A	G	G	G	171	14	CASP4	4	4
MUC5B	727897	broad.mit.edu	37	11	1157860	1157860	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1157860C>A	uc009ycr.1	+	c.927C>A	c.(925-927)CAC>CAA	p.H309Q		NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	300					cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)										0.108911	9.250639	24.557724	11	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1157860	1157860	10373	11	C	A	A	A	209	17	MUC5B	2	2
TRIM29	23650	broad.mit.edu	37	11	120008510	120008510	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:120008510C>A	uc001pwz.2	-	c.230G>T	c.(229-231)CGA>CTA	p.R77L	TRIM29_uc001pxa.2_Non-coding_Transcript	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	77					transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)	3		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)										0.223176	109.095473	125.505482	52	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120008510	120008510	17047	11	C	A	A	A	403	31	TRIM29	1	1
OR8B8	26493	broad.mit.edu	37	11	124310713	124310713	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124310713T>C	uc010sal.1	-	c.269A>G	c.(268-270)AAC>AGC	p.N90S		NM_012378	NP_036510	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B,	90	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)										0.119403	29.210271	48.25389	16	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124310713	124310713	11641	11	T	C	C	C	780	60	OR8B8	4	4
MUC5B	727897	broad.mit.edu	37	11	1271072	1271072	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1271072C>A	uc009ycr.1	+	c.14381C>A	c.(14380-14382)ACC>AAC	p.T4794N	MUC5B_uc001ltb.2_Missense_Mutation_p.T4324N	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4321	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)										0.125628	32.624946	59.874558	25	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1271072	1271072	10373	11	C	A	A	A	234	18	MUC5B	2	2
C11orf45	219833	broad.mit.edu	37	11	128772478	128772478	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128772478G>A	uc001qeu.2	-	c.412C>T	c.(412-414)CAG>TAG	p.Q138*	KCNJ5_uc001qet.2_Intron|KCNJ5_uc009zck.2_Intron|C11orf45_uc009zcl.2_Nonsense_Mutation_p.Q138*|C11orf45_uc001qev.2_Nonsense_Mutation_p.Q138*	NM_145013	NP_659450	Q8TAV5	CK045_HUMAN	hypothetical protein LOC219833 precursor	138						extracellular region					0	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)										0.180328	18.985491	24.851093	11	50	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	128772478	128772478	1681	11	G	A	A	A	585	45	C11orf45	5	2
LSP1	4046	broad.mit.edu	37	11	1905755	1905755	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1905755G>T	uc001luj.2	+	c.1045G>T	c.(1045-1047)GAC>TAC	p.D349Y	LSP1_uc001lui.2_Missense_Mutation_p.D221Y|LSP1_uc001luk.2_Missense_Mutation_p.D159Y|LSP1_uc001lul.2_Missense_Mutation_p.D159Y|LSP1_uc001lum.2_Missense_Mutation_p.D159Y	NM_001013255	NP_001013273	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 2	221					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)						91				0.1	3.265588	19.270748	10	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1905755	1905755	9439	11	G	T	T	T	429	33	LSP1	2	2
SLC6A5	9152	broad.mit.edu	37	11	20623178	20623178	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20623178G>T	uc001mqd.2	+	c.507G>T	c.(505-507)GTG>GTT	p.V169V	SLC6A5_uc009yic.2_5'UTR	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	169	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)	3					Glycine(DB00145)									0.103448	3.104508	12.197539	6	52	KEEP	---	---	---	---	capture		Silent	SNP	20623178	20623178	15184	11	G	T	T	T	587	46	SLC6A5	2	2
SLC6A5	9152	broad.mit.edu	37	11	20668466	20668466	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20668466C>G	uc001mqd.2	+	c.2056C>G	c.(2056-2058)CCA>GCA	p.P686A	SLC6A5_uc009yic.2_Missense_Mutation_p.P451A	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	686	Helical; Name=11; (Potential).				synaptic transmission	integral to plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)	3					Glycine(DB00145)									0.092308	8.043748	29.75671	12	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20668466	20668466	15184	11	C	G	G	G	286	22	SLC6A5	3	3
INS-IGF2	723961	broad.mit.edu	37	11	2182108	2182108	+	Missense_Mutation	SNP	C	G	G	rs80356664		TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:2182108C>G	uc001lvm.2	-	c.94G>C	c.(94-96)GGC>CGC	p.G32R	INS-IGF2_uc001lvi.2_Non-coding_Transcript|INS_uc001lvn.1_Missense_Mutation_p.G32R|INS_uc001lvo.1_Missense_Mutation_p.G32R|INS_uc009ydg.1_Missense_Mutation_p.G32R	NM_001042376	NP_001035835	Q1WM24	Q1WM24_HUMAN	insulin- insulin-like growth factor 2	32					glucose metabolic process	extracellular region	hormone activity				0		all_epithelial(84;0.00018)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.0832)|Lung(200;0.156)										0.168831	29.132571	37.124073	13	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2182108	2182108	8064	11	C	G	G	G	299	23	INS-IGF2	3	3
OR51D1	390038	broad.mit.edu	37	11	4661252	4661252	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4661252A>G	uc010qyk.1	+	c.232A>G	c.(232-234)ATG>GTG	p.M78V		NM_001004751	NP_001004751	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D,	78	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.113043	15.500904	32.487942	13	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4661252	4661252	11503	11	A	G	G	G	104	8	OR51D1	4	4
PACSIN3	29763	broad.mit.edu	37	11	47204070	47204070	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47204070C>A	uc001ndw.2	-	c.95G>T	c.(94-96)GGG>GTG	p.G32V	PACSIN3_uc001ndx.2_Missense_Mutation_p.G32V|PACSIN3_uc001ndy.2_Missense_Mutation_p.G32V|PACSIN3_uc001ndz.2_Non-coding_Transcript|PACSIN3_uc001nea.2_Non-coding_Transcript	NM_016223	NP_057307	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in	32	FCH.				endocytosis|negative regulation of endocytosis|positive regulation of membrane protein ectodomain proteolysis	cytoplasm|plasma membrane	cytoskeletal protein binding				0														0.117647	12.629986	32.171189	16	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47204070	47204070	11792	11	C	A	A	A	286	22	PACSIN3	2	2
OR4C3	256144	broad.mit.edu	37	11	48347153	48347153	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48347153G>A	uc010rhv.1	+	c.661G>A	c.(661-663)GGT>AGT	p.G221S		NM_001004702	NP_001004702	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C,	194	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.181818	40.546525	50.999941	20	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48347153	48347153	11456	11	G	A	A	A	611	47	OR4C3	2	2
OR51L1	119682	broad.mit.edu	37	11	5020771	5020771	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5020771C>A	uc010qyu.1	+	c.559C>A	c.(559-561)CTA>ATA	p.L187I		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	187	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.160976	51.33405	73.772637	33	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5020771	5020771	11512	11	C	A	A	A	415	32	OR51L1	2	2
HBD	3045	broad.mit.edu	37	11	5254211	5254211	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5254211C>A	uc001maf.1	-	c.427G>T	c.(427-429)GCT>TCT	p.A143S		NM_000519	NP_000510	P02042	HBD_HUMAN	delta globin	143			A -> D (in Fitzroy).		blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;5.69e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)					(NCIH1184-Tumor)	3				0.090323	4.823871	31.087709	14	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5254211	5254211	7261	11	C	A	A	A	338	26	HBD	2	2
OR4P4	81300	broad.mit.edu	37	11	55405957	55405957	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55405957C>G	uc010rij.1	+	c.124C>G	c.(124-126)CTC>GTC	p.L42V		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	42	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.307087	130.281094	134.492687	39	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55405957	55405957	11490	11	C	G	G	G	260	20	OR4P4	3	3
OR5L1	219437	broad.mit.edu	37	11	55579766	55579766	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55579766C>A	uc001nhw.1	+	c.824C>A	c.(823-825)ACC>AAC	p.T275N		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	275	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		all_epithelial(135;0.208)												0.235294	56.974938	63.493741	24	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55579766	55579766	11580	11	C	A	A	A	234	18	OR5L1	2	2
OR5M3	219482	broad.mit.edu	37	11	56237426	56237426	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56237426A>T	uc010rjk.1	-	c.548T>A	c.(547-549)ATC>AAC	p.I183N		NM_001004742	NP_001004742	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M,	183	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.149038	49.393585	73.986902	31	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56237426	56237426	11585	11	A	T	T	T	156	12	OR5M3	3	3
MS4A6E	245802	broad.mit.edu	37	11	60102398	60102398	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60102398C>G	uc001npd.2	+	c.30C>G	c.(28-30)ACC>ACG	p.T10T		NM_139249	NP_640342	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member	10	Cytoplasmic (Potential).					integral to membrane	receptor activity				0														0.141304	47.023214	69.869224	26	158	KEEP	---	---	---	---	capture		Silent	SNP	60102398	60102398	10258	11	C	G	G	G	262	21	MS4A6E	3	3
CNGA4	1262	broad.mit.edu	37	11	6262724	6262724	+	Silent	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6262724T>A	uc001mco.2	+	c.981T>A	c.(979-981)CCT>CCA	p.P327P	CNGA4_uc010raa.1_Silent_p.P96P|CNGA4_uc001mcn.2_Silent_p.P287P	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	327	Cytoplasmic (Potential).				response to stimulus|sensory perception of smell		cAMP binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.086957	2.911894	26.730384	12	126	KEEP	---	---	---	---	capture		Silent	SNP	6262724	6262724	3737	11	T	A	A	A	704	55	CNGA4	3	3
STARD10	10809	broad.mit.edu	37	11	72492187	72492187	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:72492187G>A	uc001osy.2	-	c.40C>T	c.(40-42)CGG>TGG	p.R14W	ARAP1_uc001osv.2_Intron|STARD10_uc001osz.3_Missense_Mutation_p.R14W|STARD10_uc001ota.2_Missense_Mutation_p.R14W|STARD10_uc001otb.2_Missense_Mutation_p.R14W	NM_006645	NP_006636	Q9Y365	PCTL_HUMAN	START domain containing 10	14	START.										0			BRCA - Breast invasive adenocarcinoma(5;7.08e-07)											0.122807	14.172001	30.050351	14	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72492187	72492187	15774	11	G	A	A	A	480	37	STARD10	1	1
CTSC	1075	broad.mit.edu	37	11	88027474	88027474	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:88027474C>T	uc001pck.3	-	c.1092G>A	c.(1090-1092)TTG>TTA	p.L364L	CTSC_uc001pcl.3_Silent_p.L216L	NM_001814	NP_001805	P53634	CATC_HUMAN	cathepsin C isoform a preproprotein	364					immune response	lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												0.179245	77.41577	97.946423	38	174	KEEP	---	---	---	---	capture		Silent	SNP	88027474	88027474	4190	11	C	T	T	T	272	21	CTSC	2	2
FAT3	120114	broad.mit.edu	37	11	92531802	92531802	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92531802G>A	uc001pdj.3	+	c.5623G>A	c.(5623-5625)GAT>AAT	p.D1875N		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1875	Cadherin 16.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.117647	8.945054	18.728026	8	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92531802	92531802	5927	11	G	A	A	A	429	33	FAT3	2	2
HSPB8	26353	broad.mit.edu	37	12	119617367	119617367	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:119617367G>T	uc001txb.2	+	c.250G>T	c.(250-252)GAG>TAG	p.E84*	HSPB8_uc001txc.2_Nonsense_Mutation_p.E84*	NM_014365	NP_055180	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	84					cell death|response to heat	cytoplasm|nucleus	identical protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)								p.E84K(PCM6-Tumor)|p.E84K(KMM1-Tumor)	174				0.108108	5.642732	16.916831	8	66	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	119617367	119617367	7723	12	G	T	T	T	481	37	HSPB8	5	1
TMEM132B	114795	broad.mit.edu	37	12	126139092	126139092	+	Nonsense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:126139092A>T	uc001uhe.1	+	c.3073A>T	c.(3073-3075)AAG>TAG	p.K1025*	TMEM132B_uc001uhf.1_Nonsense_Mutation_p.K537*	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	1025	Cytoplasmic (Potential).					integral to membrane				ovary(5)|large_intestine(1)|breast(1)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)										0.271186	83.55365	89.121974	32	86	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	126139092	126139092	16577	12	A	T	T	T	65	5	TMEM132B	5	3
POLE	5426	broad.mit.edu	37	12	133256133	133256133	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:133256133C>G	uc001uks.1	-	c.528G>C	c.(526-528)AAG>AAC	p.K176N	POLE_uc010tbq.1_Non-coding_Transcript|POLE_uc009zyu.1_Missense_Mutation_p.K149N	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	176					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)										0.117318	34.648857	60.418111	21	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133256133	133256133	12624	12	C	G	G	G	415	32	POLE	3	3
C12orf36	283422	broad.mit.edu	37	12	13529158	13529158	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:13529158C>A	uc001rbs.1	-	c.182G>T	c.(181-183)AGC>ATC	p.S61I		NM_182558	NP_872364			hypothetical protein LOC283422												0				BRCA - Breast invasive adenocarcinoma(232;0.198)										0.051546	-25.092937	16.200612	10	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13529158	13529158	1727	12	C	A	A	A	312	24	C12orf36	2	2
PDE6H	5149	broad.mit.edu	37	12	15134401	15134401	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:15134401G>A	uc001rcr.2	+	c.243G>A	c.(241-243)GGG>GGA	p.G81G		NM_006205	NP_006196	Q13956	CNCG_HUMAN	phosphodiesterase 6H	81					visual perception		3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|enzyme inhibitor activity			ovary(1)	1														0.242187	71.153749	78.919515	31	97	KEEP	---	---	---	---	capture		Silent	SNP	15134401	15134401	12071	12	G	A	A	A	522	41	PDE6H	2	2
GYS2	2998	broad.mit.edu	37	12	21713354	21713354	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21713354T>A	uc001rfb.2	-	c.1135A>T	c.(1135-1137)ACC>TCC	p.T379S		NM_021957	NP_068776	P54840	GYS2_HUMAN	glycogen synthase 2	379					glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity				0						Colon(149;9 1820 3690 10544 50424)								0.096026	15.402732	64.793304	29	273	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21713354	21713354	7193	12	T	A	A	A	780	60	GYS2	3	3
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:25398285C>A	uc001rgp.1	-	c.34G>T	c.(34-36)GGT>TGT	p.G12C	KRAS_uc001rgq.1_Missense_Mutation_p.G12C|KRAS_uc001rgr.2_Non-coding_Transcript	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	12	GTP.		G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12C(2374)|p.G12S(1078)|p.G12R(674)|p.G12?(50)|p.G12F(33)|p.G12D(15)|p.G12N(6)|p.G12V(6)|p.G12L(5)|p.G12I(3)|p.G12W(3)|p.G12A(2)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12_G13insG(1)		large_intestine(11742)|pancreas(3256)|lung(2694)|biliary_tract(514)|ovary(437)|endometrium(339)|haematopoietic_and_lymphoid_tissue(303)|stomach(179)|thyroid(145)|prostate(85)|soft_tissue(75)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|breast(27)|liver(21)|testis(17)|oesophagus(15)|central_nervous_system(8)|peritoneum(5)|kidney(5)|salivary_gland(5)|thymus(5)|eye(4)|gastrointestinal_tract_(site_indeterminate)(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	20148	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12C(CALU1_LUNG)|G12C(NCIH2030_LUNG)|G12C(LU99_LUNG)|G12C(NCIH1792_LUNG)|G12R(KP2_PANCREAS)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(NCIH2122_LUNG)|G12C(NCIH358_LUNG)|G12R(PSN1_PANCREAS)|G12C(KYSE410_OESOPHAGUS)|G12S(A549_LUNG)|G12R(HUPT3_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12C(HCC44_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(SW1463_LARGE_INTESTINE)|G12C(NCIH23_LUNG)|G12C(LU65_LUNG)|G12C(NCIH1373_LUNG)|G12C(MIAPACA2_PANCREAS)|G12R(HS274T_BREAST)|G12S(LS123_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(OV56_OVARY)|G12C(IALM_LUNG)	119	p.G12R(PSN1-Tumor)|p.G12C(NCIH1373-Tumor)|p.G12C(NCIH1792-Tumor)|p.G12S(KMS20-Tumor)|p.G12C(HCC44-Tumor)|p.G12C(HCC1171-Tumor)|p.G12C(SW837-Tumor)|p.G12C(LU65-Tumor)|p.G12R(HUPT3-Tumor)|p.G12S(A549-Tumor)|p.G12C(NCIH2122-Tumor)|p.G12R(KP2-Tumor)|p.G12C(OV56-Tumor)|p.G12C(IALM-Tumor)|p.G12C(SW1463-Tumor)|p.G12C(SW1573-Tumor)|p.G12R(NCIH1339-Tumor)|p.G12C(NCIH23-Tumor)|p.G12C(MIAPACA2-Tumor)|p.G12C(CALU1-Tumor)|p.G12C(NCIH2030-Tumor)|p.G12S(LS123-Tumor)|p.G12C(KYSE410-Tumor)|p.G12C(UMUC3-Tumor)|p.G12C(NCIH2291-Tumor)|p.G12R(TCCPAN2-Tumor)|p.G12C(KHM1B-Tumor)|p.G12C(LU99-Tumor)|p.G12C(NCIH358-Tumor)|p.G12C(NCIH1385-Tumor)|p.G12R(CAL62-Tumor)	262	TSP Lung(1;<1E-8)|Multiple Myeloma(2;<1E-6)			0.196078	20.517893	24.910964	10	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25398285	25398285	8753	12	C	A	A	A	273	21	KRAS	2	2
RASSF8	11228	broad.mit.edu	37	12	26217434	26217434	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:26217434G>C	uc001rgx.2	+	c.107G>C	c.(106-108)CGA>CCA	p.R36P	RASSF8_uc001rgy.2_Missense_Mutation_p.R36P|RASSF8_uc001rgz.2_Missense_Mutation_p.R36P|RASSF8_uc009zjd.1_Missense_Mutation_p.R36P|RASSF8_uc009zje.1_Missense_Mutation_p.R36P	NM_007211	NP_009142	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family	36	Ras-associating.				signal transduction						0	Colorectal(261;0.0847)													0.24424	158.776215	171.702451	53	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26217434	26217434	13553	12	G	C	C	C	481	37	RASSF8	3	3
OVCH1	341350	broad.mit.edu	37	12	29598250	29598250	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29598250C>T	uc001rix.1	-	c.2842G>A	c.(2842-2844)GGT>AGT	p.G948S		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	948	CUB 3.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)													0.240602	87.534938	95.699343	32	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29598250	29598250	11736	12	C	T	T	T	312	24	OVCH1	2	2
OVCH1	341350	broad.mit.edu	37	12	29598303	29598303	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29598303G>T	uc001rix.1	-	c.2789C>A	c.(2788-2790)ACT>AAT	p.T930N		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	930	CUB 3.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)													0.224719	49.551539	55.749873	20	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29598303	29598303	11736	12	G	T	T	T	468	36	OVCH1	2	2
DDX11	1663	broad.mit.edu	37	12	31253967	31253967	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:31253967T>G	uc001rjt.1	+	c.1955T>G	c.(1954-1956)GTG>GGG	p.V652G	DDX11_uc001rjr.1_Missense_Mutation_p.V652G|DDX11_uc001rjs.1_Missense_Mutation_p.V652G|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Missense_Mutation_p.V652G|DDX11_uc001rjw.1_Missense_Mutation_p.V626G|DDX11_uc009zjn.1_Non-coding_Transcript|DDX11_uc009zjo.1_5'Flank	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	652					G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.197452	156.922336	183.790361	62	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31253967	31253967	4514	12	T	G	G	G	767	59	DDX11	4	4
LRRK2	120892	broad.mit.edu	37	12	40689416	40689416	+	Silent	SNP	A	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:40689416A>C	uc001rmg.3	+	c.3066A>C	c.(3064-3066)GCA>GCC	p.A1022A	LRRK2_uc001rmh.1_Silent_p.A644A|LRRK2_uc009zjw.2_5'UTR	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1022	LRR 2.				activation of MAPKK activity|determination of adult lifespan|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(11)|lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)|stomach(1)|urinary_tract(1)|pancreas(1)	18	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)								1771				0.147541	41.233895	55.882433	18	104	KEEP	---	---	---	---	capture		Silent	SNP	40689416	40689416	9409	12	A	C	C	C	67	6	LRRK2	4	4
ADAMTS20	80070	broad.mit.edu	37	12	43777518	43777518	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43777518C>T	uc010skx.1	-	c.4640G>A	c.(4639-4641)TGT>TAT	p.C1547Y		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1547	TSP type-1 13.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.217391	62.275784	72.440534	30	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43777518	43777518	267	12	C	T	T	T	221	17	ADAMTS20	2	2
NELL2	4753	broad.mit.edu	37	12	45000952	45000952	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45000952C>A	uc010skz.1	-	c.1813G>T	c.(1813-1815)GAC>TAC	p.D605Y	NELL2_uc001rof.3_Missense_Mutation_p.D554Y|NELL2_uc001rog.2_Missense_Mutation_p.D555Y|NELL2_uc001roh.2_Missense_Mutation_p.D555Y|NELL2_uc009zkd.2_Missense_Mutation_p.D554Y|NELL2_uc010sla.1_Missense_Mutation_p.D578Y|NELL2_uc001roi.1_Missense_Mutation_p.D555Y|NELL2_uc010slb.1_Missense_Mutation_p.D554Y	NM_001145107	NP_001138579	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform a	555	EGF-like 5; calcium-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			central_nervous_system(1)	1	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)										0.261261	65.648152	71.360044	29	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45000952	45000952	10733	12	C	A	A	A	286	22	NELL2	2	2
ANO6	196527	broad.mit.edu	37	12	45782068	45782068	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45782068G>A	uc010slf.1	+	c.1353G>A	c.(1351-1353)GTG>GTA	p.V451V	ANO6_uc001roo.2_Silent_p.V430V|ANO6_uc010sld.1_Silent_p.V430V|ANO6_uc010sle.1_Silent_p.V430V|ANO6_uc010slg.1_Silent_p.V412V	NM_001142678	NP_001136150	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform b	430	Cytoplasmic (Potential).				activation of blood coagulation via clotting cascade	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2														0.218009	97.53612	113.008948	46	165	KEEP	---	---	---	---	capture		Silent	SNP	45782068	45782068	709	12	G	A	A	A	574	45	ANO6	2	2
KCNA6	3742	broad.mit.edu	37	12	4920245	4920245	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:4920245G>T	uc001qng.2	+	c.1038G>T	c.(1036-1038)CTG>CTT	p.L346L		NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related	346	Helical; Voltage-sensor; Name=Segment S4; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|skin(1)	2														0.314815	42.769895	44.40986	17	37	KEEP	---	---	---	---	capture		Silent	SNP	4920245	4920245	8312	12	G	T	T	T	600	47	KCNA6	2	2
MLL2	8085	broad.mit.edu	37	12	49436374	49436374	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49436374C>G	uc001rta.3	-	c.5837G>C	c.(5836-5838)GGC>GCC	p.G1946A		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1946					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|promoter binding|protein binding|zinc ion binding			kidney(16)|lung(4)|skin(4)|ovary(3)|pancreas(2)	29														0.296703	89.70073	93.057452	27	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49436374	49436374	10011	12	C	G	G	G	338	26	MLL2	3	3
GLI1	2735	broad.mit.edu	37	12	57864243	57864243	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57864243G>A	uc001snx.2	+	c.1720G>A	c.(1720-1722)GGA>AGA	p.G574R	GLI1_uc009zpq.2_Missense_Mutation_p.G446R	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	574					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of gene-specific transcription|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	promoter binding|transcription activator activity|zinc ion binding			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	14			GBM - Glioblastoma multiforme(3;3.99e-32)			Pancreas(157;841 1936 10503 41495 50368)				277				0.254658	98.49785	107.294465	41	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57864243	57864243	6705	12	G	A	A	A	611	47	GLI1	2	2
CHD4	1108	broad.mit.edu	37	12	6697022	6697022	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6697022C>G	uc001qpp.2	-	c.3550G>C	c.(3550-3552)GTG>CTG	p.V1184L	CHD4_uc001qpn.2_Missense_Mutation_p.V1180L|CHD4_uc001qpo.2_Missense_Mutation_p.V1187L	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1187	Helicase C-terminal.				chromatin assembly or disassembly|chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	chromatin|microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|chromatin binding|DNA binding|zinc ion binding			central_nervous_system(2)	2						Colon(32;586 792 4568 16848 45314)								0.058537	-10.152697	31.685185	12	193	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6697022	6697022	3461	12	C	G	G	G	234	18	CHD4	3	3
SLC6A15	55117	broad.mit.edu	37	12	85279239	85279239	+	Silent	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85279239A>T	uc001szv.2	-	c.549T>A	c.(547-549)CCT>CCA	p.P183P	SLC6A15_uc010sul.1_Silent_p.P76P|SLC6A15_uc001szy.2_Silent_p.P183P	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	183	Extracellular (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3														0.268908	74.347111	80.083971	32	87	KEEP	---	---	---	---	capture		Silent	SNP	85279239	85279239	15175	12	A	T	T	T	28	3	SLC6A15	3	3
DUSP6	1848	broad.mit.edu	37	12	89743161	89743161	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:89743161T>A	uc001tay.2	-	c.1016A>T	c.(1015-1017)CAG>CTG	p.Q339L	DUSP6_uc001taz.2_Missense_Mutation_p.Q193L	NM_001946	NP_001937	Q16828	DUS6_HUMAN	dual specificity phosphatase 6 isoform a	339	Tyrosine-protein phosphatase.				dorsal/ventral pattern formation|inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|nerve growth factor receptor signaling pathway|positive regulation of apoptosis|regulation of endodermal cell fate specification|regulation of fibroblast growth factor receptor signaling pathway|regulation of heart growth|response to nitrosative stress|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0						Colon(132;3456 5224)				159				0.261224	163.09009	175.731825	64	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89743161	89743161	5014	12	T	A	A	A	715	55	DUSP6	3	3
NALCN	259232	broad.mit.edu	37	13	101795440	101795440	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101795440G>A	uc001vox.1	-	c.2109C>T	c.(2107-2109)ATC>ATT	p.I703I	NALCN_uc001voy.2_Silent_p.I418I	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	703	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.133333	29.789072	53.280164	24	156	KEEP	---	---	---	---	capture		Silent	SNP	101795440	101795440	10544	13	G	A	A	A	473	37	NALCN	1	1
ARGLU1	55082	broad.mit.edu	37	13	107211830	107211830	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:107211830C>T	uc001vqk.3	-	c.523G>A	c.(523-525)GAA>AAA	p.E175K	ARGLU1_uc010age.1_Missense_Mutation_p.E8K	NM_018011	NP_060481	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1	175	Glu-rich.										0	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)													0.147239	36.197281	55.681905	24	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107211830	107211830	871	13	C	T	T	T	416	32	ARGLU1	2	2
ARHGEF7	8874	broad.mit.edu	37	13	111896616	111896616	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:111896616G>T	uc001vrs.2	+	c.988G>T	c.(988-990)GTA>TTA	p.V330L	ARHGEF7_uc001vrr.2_Missense_Mutation_p.V309L|ARHGEF7_uc001vrt.2_Missense_Mutation_p.V280L|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Missense_Mutation_p.V152L|ARHGEF7_uc001vrv.3_Missense_Mutation_p.V152L|ARHGEF7_uc001vrw.3_Missense_Mutation_p.V152L|ARHGEF7_uc001vrx.3_Missense_Mutation_p.V152L|ARHGEF7_uc010tjo.1_Missense_Mutation_p.V227L|ARHGEF7_uc010tjp.1_Missense_Mutation_p.V74L|ARHGEF7_uc010agn.1_Missense_Mutation_p.V74L	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	330	DH.				apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)							707				0.116883	12.420373	23.536344	9	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111896616	111896616	926	13	G	T	T	T	520	40	ARHGEF7	1	1
ARHGEF7	8874	broad.mit.edu	37	13	111929984	111929984	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:111929984G>C	uc001vrs.2	+	c.1533G>C	c.(1531-1533)TTG>TTC	p.L511F	ARHGEF7_uc001vrr.2_Missense_Mutation_p.L490F|ARHGEF7_uc001vrt.2_Missense_Mutation_p.L461F|ARHGEF7_uc010tjn.1_Non-coding_Transcript|ARHGEF7_uc001vru.1_Missense_Mutation_p.L333F|ARHGEF7_uc001vrv.3_Missense_Mutation_p.L333F|ARHGEF7_uc001vrw.3_Missense_Mutation_p.L333F|ARHGEF7_uc001vrx.3_Missense_Mutation_p.L333F|ARHGEF7_uc010tjo.1_Missense_Mutation_p.L408F|ARHGEF7_uc010tjp.1_Missense_Mutation_p.L255F	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	511	PH.				apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)							707				0.174312	46.136674	57.086078	19	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111929984	111929984	926	13	G	C	C	C	620	48	ARHGEF7	3	3
MTMR6	9107	broad.mit.edu	37	13	25832811	25832811	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25832811C>A	uc001uqf.3	-	c.746G>T	c.(745-747)AGA>ATA	p.R249I	MTMR6_uc001uqe.1_Missense_Mutation_p.R249I	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	249	Myotubularin phosphatase.|Substrate binding (By similarity).					cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)										0.107143	3.906082	12.486861	6	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25832811	25832811	10340	13	C	A	A	A	416	32	MTMR6	2	2
GPR12	2835	broad.mit.edu	37	13	27333529	27333529	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:27333529G>A	uc010aal.2	-	c.436C>T	c.(436-438)CTG>TTG	p.L146L	GPR12_uc010tdl.1_5'UTR	NM_005288	NP_005279	P47775	GPR12_HUMAN	G protein-coupled receptor 12	146	Cytoplasmic (Potential).					integral to plasma membrane					0	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)										0.173554	42.893329	55.073389	21	100	KEEP	---	---	---	---	capture		Silent	SNP	27333529	27333529	6909	13	G	A	A	A	425	33	GPR12	2	2
USPL1	10208	broad.mit.edu	37	13	31205085	31205085	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31205085G>T	uc001utc.2	+	c.342G>T	c.(340-342)AAG>AAT	p.K114N	USPL1_uc001utb.2_De_novo_Start_OutOfFrame|USPL1_uc001utd.2_Intron	NM_005800	NP_005791	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	114					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			pancreas(1)	1		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		Ovarian(60;318 1180 1554 28110 31601)								0.176471	30.978618	41.05134	18	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31205085	31205085	17656	13	G	T	T	T	451	35	USPL1	2	2
NAA16	79612	broad.mit.edu	37	13	41892955	41892955	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:41892955G>C	uc001uyf.2	+	c.153G>C	c.(151-153)ATG>ATC	p.M51I	NAA16_uc010tfg.1_Non-coding_Transcript|NAA16_uc001uye.3_Missense_Mutation_p.M51I|NAA16_uc001uyd.3_Missense_Mutation_p.M51I	NM_024561	NP_078837	Q6N069	NAA16_HUMAN	NMDA receptor regulated 1-like protein isoform	51	TPR 1.				N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1														0.118421	14.210252	25.104261	9	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41892955	41892955	10514	13	G	C	C	C	585	45	NAA16	3	3
ESD	2098	broad.mit.edu	37	13	47354087	47354087	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:47354087C>A	uc001vbn.2	-	c.583G>T	c.(583-585)GAT>TAT	p.D195Y	ESD_uc001vbo.2_Missense_Mutation_p.D195Y|ESD_uc001vbp.1_Missense_Mutation_p.D53Y	NM_001984	NP_001975	P10768	ESTD_HUMAN	esterase D/formylglutathione hydrolase	195						cytoplasmic membrane-bounded vesicle	carboxylesterase activity|S-formylglutathione hydrolase activity			ovary(1)	1		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)									0.194245	50.434261	62.569208	27	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47354087	47354087	5443	13	C	A	A	A	416	32	ESD	2	2
DIAPH3	81624	broad.mit.edu	37	13	60667825	60667826	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:60667825_60667826CC>AA	uc001vht.2	-	c.431_432GG>TT	c.(430-432)CGG>CTT	p.R144L	DIAPH3_uc001vhw.1_Missense_Mutation_p.R133L|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Missense_Mutation_p.R74L	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	144	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)										0.075949	-2.61827	11.949212	6	73	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	60667825	60667826	4699	13	CC	AA	AA	AA	275	22	DIAPH3	2	2
GPC6	10082	broad.mit.edu	37	13	94482465	94482465	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:94482465G>T	uc001vlt.2	+	c.378G>T	c.(376-378)CGG>CGT	p.R126R	GPC6_uc010tig.1_Silent_p.R126R|GPC6_uc001vlu.1_Silent_p.R56R	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor	126						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)												0.107843	6.74786	22.311452	11	91	KEEP	---	---	---	---	capture		Silent	SNP	94482465	94482465	6876	13	G	T	T	T	522	41	GPC6	2	2
DCT	1638	broad.mit.edu	37	13	95121061	95121061	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:95121061G>T	uc010afh.2	-	c.534C>A	c.(532-534)AAC>AAA	p.N178K	DCT_uc001vlv.3_Missense_Mutation_p.N178K	NM_001129889	NP_001123361	P40126	TYRP2_HUMAN	dopachrome tautomerase isoform 2	178	Lumenal, melanosome (Potential).				epidermis development|melanin biosynthetic process from tyrosine	cytosol|integral to membrane|melanosome membrane|microsome	copper ion binding|dopachrome isomerase activity|oxidoreductase activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)										0.195035	107.731369	132.228568	55	227	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95121061	95121061	4475	13	G	T	T	T	464	36	DCT	2	2
OR11H4	390442	broad.mit.edu	37	14	20711267	20711267	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20711267G>T	uc010tld.1	+	c.317G>T	c.(316-318)GGG>GTG	p.G106V		NM_001004479	NP_001004479	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H,	106	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)										0.223214	102.438285	118.218565	50	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20711267	20711267	11334	14	G	T	T	T	559	43	OR11H4	2	2
SALL2	6297	broad.mit.edu	37	14	21992890	21992890	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21992890G>A	uc001wbe.2	-	c.972C>T	c.(970-972)ACC>ACT	p.T324T	SALL2_uc010tly.1_Silent_p.T322T|SALL2_uc010tlz.1_Silent_p.T187T|SALL2_uc001wbf.3_Intron|SALL2_uc010tma.1_Silent_p.T189T|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	324							DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)										0.2375	41.444637	46.530157	19	61	KEEP	---	---	---	---	capture		Silent	SNP	21992890	21992890	14291	14	G	A	A	A	600	47	SALL2	2	2
SLC7A7	9056	broad.mit.edu	37	14	23242826	23242826	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23242826G>T	uc001wgr.3	-	c.1529C>A	c.(1528-1530)TCT>TAT	p.S510Y	SLC7A7_uc001wgs.3_Missense_Mutation_p.S510Y|SLC7A7_uc001wgt.3_Missense_Mutation_p.S510Y|SLC7A7_uc001wgu.3_Missense_Mutation_p.S510Y|SLC7A7_uc001wgv.3_Missense_Mutation_p.S510Y	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7	510					blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)										0.196078	38.33981	47.124394	20	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23242826	23242826	15200	14	G	T	T	T	429	33	SLC7A7	2	2
MYH6	4624	broad.mit.edu	37	14	23853903	23853903	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23853903C>T	uc001wjv.2	-	c.5313G>A	c.(5311-5313)CTG>CTA	p.L1771L		NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	1771	Potential.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)	3	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)										0.103604	11.749355	46.500819	23	199	KEEP	---	---	---	---	capture		Silent	SNP	23853903	23853903	10433	14	C	T	T	T	366	29	MYH6	2	2
NID2	22795	broad.mit.edu	37	14	52507529	52507529	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:52507529C>G	uc001wzo.2	-	c.1866G>C	c.(1864-1866)CCG>CCC	p.P622P	NID2_uc010tqs.1_Silent_p.P622P|NID2_uc010tqt.1_Silent_p.P622P|NID2_uc001wzp.2_Silent_p.P622P	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	622	Nidogen G2 beta-barrel.				bioluminescence|protein-chromophore linkage	basement membrane|membrane	calcium ion binding|collagen binding			breast(2)|pancreas(2)|ovary(1)|liver(1)	6	Breast(41;0.0639)|all_epithelial(31;0.123)													0.277228	160.72148	169.737596	56	146	KEEP	---	---	---	---	capture		Silent	SNP	52507529	52507529	10816	14	C	G	G	G	288	23	NID2	3	3
WDR89	112840	broad.mit.edu	37	14	64065848	64065848	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64065848T>C	uc001xgh.2	-	c.813A>G	c.(811-813)GAA>GAG	p.E271E	WDR89_uc001xgi.2_Silent_p.E271E	NM_001008726	NP_001008726	Q96FK6	WDR89_HUMAN	WD repeat domain 89	271											0				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)										0.210526	179.834563	203.397361	64	240	KEEP	---	---	---	---	capture		Silent	SNP	64065848	64065848	17910	14	T	C	C	C	725	56	WDR89	4	4
LTBP2	4053	broad.mit.edu	37	14	75052556	75052556	+	Splice_Site_SNP	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75052556C>A	uc001xqa.2	-	c.830_splice	c.e3+1	p.G277_splice		NM_000428	NP_000419			latent transforming growth factor beta binding						protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)										0.216216	37.563556	43.059858	16	58	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	75052556	75052556	9450	14	C	A	A	A	234	18	LTBP2	5	2
FLVCR2	55640	broad.mit.edu	37	14	76108196	76108196	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:76108196G>C	uc001xrs.2	+	c.1464G>C	c.(1462-1464)AAG>AAC	p.K488N	FLVCR2_uc010tvd.1_Missense_Mutation_p.K283N	NM_017791	NP_060261	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular	488	Helical; (Potential).				transmembrane transport	integral to membrane|plasma membrane	heme binding|heme transporter activity				0				BRCA - Breast invasive adenocarcinoma(234;0.029)										0.068702	-1.238466	23.958365	9	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76108196	76108196	6188	14	G	C	C	C	451	35	FLVCR2	3	3
ANGEL1	23357	broad.mit.edu	37	14	77273815	77273815	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77273815G>A	uc001xsv.2	-	c.907C>T	c.(907-909)CAT>TAT	p.H303Y	ANGEL1_uc010tvf.1_Intron	NM_015305	NP_056120	Q9UNK9	ANGE1_HUMAN	angel homolog 1	303										ovary(2)|central_nervous_system(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)										0.323529	54.518761	56.402667	22	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77273815	77273815	611	14	G	A	A	A	585	45	ANGEL1	2	2
SERPINA6	866	broad.mit.edu	37	14	94776131	94776131	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94776131C>A	uc001ycv.2	-	c.826G>T	c.(826-828)GTC>TTC	p.V276F	SERPINA6_uc010auv.2_Non-coding_Transcript	NM_001756	NP_001747	P08185	CBG_HUMAN	corticosteroid binding globulin precursor	276					regulation of proteolysis|transport	extracellular space	serine-type endopeptidase inhibitor activity|steroid binding			skin(2)|ovary(1)|central_nervous_system(1)	4		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)									0.112195	19.373189	49.838448	23	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94776131	94776131	14581	14	C	A	A	A	260	20	SERPINA6	2	2
C14orf49	161176	broad.mit.edu	37	14	95910860	95910860	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95910860C>A	uc001yei.3	-	c.1738G>T	c.(1738-1740)GAC>TAC	p.D580Y	C14orf49_uc010avi.2_Missense_Mutation_p.D580Y|C14orf49_uc001yej.1_Missense_Mutation_p.D580Y	NM_152592	NP_689805	Q6ZMZ3	SYNE3_HUMAN	nesprin-3	580	Cytoplasmic (Potential).				cytoskeletal anchoring at nuclear membrane	integral to membrane|nuclear outer membrane|SUN-KASH complex	actin binding			central_nervous_system(1)	1		all_cancers(154;0.0937)		COAD - Colon adenocarcinoma(157;0.245)										0.153846	18.68592	29.123811	14	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95910860	95910860	1826	14	C	A	A	A	390	30	C14orf49	2	2
OR4M2	390538	broad.mit.edu	37	15	22368980	22368980	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:22368980C>A	uc010tzu.1	+	c.405C>A	c.(403-405)ATC>ATA	p.I135I	LOC727924_uc001yua.2_Non-coding_Transcript|LOC727924_uc001yub.1_Intron|OR4N4_uc001yuc.1_Intron	NM_001004719	NP_001004719	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M,	135	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)										0.058394	-66.705872	73.366517	40	645	KEEP	---	---	---	---	capture		Silent	SNP	22368980	22368980	11486	15	C	A	A	A	369	29	OR4M2	2	2
C15orf2	23742	broad.mit.edu	37	15	24923924	24923924	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24923924T>G	uc001ywo.2	+	c.2910T>G	c.(2908-2910)AGT>AGG	p.S970R		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	970					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)						443				0.145455	28.925773	42.240467	16	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24923924	24923924	1834	15	T	G	G	G	764	59	C15orf2	4	4
OCA2	4948	broad.mit.edu	37	15	28211878	28211878	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:28211878A>T	uc001zbh.3	-	c.1594T>A	c.(1594-1596)TGG>AGG	p.W532R	OCA2_uc010ayv.2_Missense_Mutation_p.W508R	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	532	Cytoplasmic (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										0.157303	20.788226	30.767317	14	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28211878	28211878	11220	15	A	T	T	T	91	7	OCA2	3	3
HERC2	8924	broad.mit.edu	37	15	28483346	28483346	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:28483346C>A	uc001zbj.2	-	c.3766G>T	c.(3766-3768)GAC>TAC	p.D1256Y		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1256	Cytochrome b5 heme-binding.				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(2)|central_nervous_system(1)	11		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)						1580				0.120879	11.054202	23.885586	11	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28483346	28483346	7341	15	C	A	A	A	416	32	HERC2	2	2
RYR3	6263	broad.mit.edu	37	15	34115267	34115267	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:34115267C>A	uc001zhi.2	+	c.11066C>A	c.(11065-11067)TCT>TAT	p.S3689Y	RYR3_uc010bar.2_Missense_Mutation_p.S3684Y	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3689					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.15	16.940719	26.345298	12	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34115267	34115267	14250	15	C	A	A	A	416	32	RYR3	2	2
TRIM69	140691	broad.mit.edu	37	15	45059966	45059966	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45059966A>T	uc001zuf.2	+	c.1499A>T	c.(1498-1500)CAG>CTG	p.Q500L	TRIM69_uc001zui.1_Missense_Mutation_p.Q296L|TRIM69_uc010bdy.1_Missense_Mutation_p.Q279L|TRIM69_uc001zug.1_Missense_Mutation_p.Q500L|TRIM69_uc001zuh.1_Missense_Mutation_p.Q341L	NM_182985	NP_892030	Q86WT6	TRI69_HUMAN	tripartite motif-containing 69 isoform a	500	B30.2/SPRY.				apoptosis	nuclear speck	zinc ion binding				0		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		Pancreas(84;519 1450 1802 20427 34706)								0.252427	59.795186	65.533336	26	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45059966	45059966	17091	15	A	T	T	T	91	7	TRIM69	3	3
SEMA6D	80031	broad.mit.edu	37	15	48063015	48063015	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48063015G>A	uc010bek.2	+	c.2255G>A	c.(2254-2256)GGA>GAA	p.G752E	SEMA6D_uc001zvw.2_Missense_Mutation_p.G690E|SEMA6D_uc001zvy.2_Missense_Mutation_p.G752E|SEMA6D_uc001zvz.2_Missense_Mutation_p.G696E|SEMA6D_uc001zwa.2_3'UTR|SEMA6D_uc001zwb.2_Missense_Mutation_p.G690E|SEMA6D_uc001zwc.2_Missense_Mutation_p.G677E	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor	752	Cytoplasmic (Potential).				axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			breast(1)	1		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)										0.226562	69.639124	78.403917	29	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48063015	48063015	14528	15	G	A	A	A	533	41	SEMA6D	2	2
CGNL1	84952	broad.mit.edu	37	15	57731244	57731244	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:57731244A>G	uc002aeg.2	+	c.1047A>G	c.(1045-1047)TCA>TCG	p.S349S	CGNL1_uc010bfw.2_Silent_p.S349S	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	349	Head.					myosin complex|tight junction	motor activity			ovary(4)|central_nervous_system(1)	5				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)										0.170732	30.402277	38.808114	14	68	KEEP	---	---	---	---	capture		Silent	SNP	57731244	57731244	3437	15	A	G	G	G	54	5	CGNL1	4	4
TLN2	83660	broad.mit.edu	37	15	62993362	62993362	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62993362C>G	uc002alb.3	+	c.1645C>G	c.(1645-1647)CAA>GAA	p.Q549E		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	549					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cell-cell junction|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(4)|breast(2)	6														0.223301	66.341167	73.541381	23	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62993362	62993362	16478	15	C	G	G	G	377	29	TLN2	3	3
AAGAB	79719	broad.mit.edu	37	15	67500916	67500916	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:67500916C>G	uc002aqk.3	-	c.699G>C	c.(697-699)CAG>CAC	p.Q233H	AAGAB_uc002aql.2_Missense_Mutation_p.Q124H|AAGAB_uc010uju.1_Missense_Mutation_p.Q124H	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34	233					protein transport	cytoplasm					0														0.064516	-3.34818	8.872175	4	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67500916	67500916	16	15	C	G	G	G	311	24	AAGAB	3	3
ITGA11	22801	broad.mit.edu	37	15	68631901	68631901	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:68631901G>A	uc010bib.2	-	c.1213C>T	c.(1213-1215)CCT>TCT	p.P405S	ITGA11_uc002ari.2_Missense_Mutation_p.P405S	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	405	FG-GAP 3.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)									0.126761	11.29971	20.889744	9	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68631901	68631901	8178	15	G	A	A	A	533	41	ITGA11	2	2
PTPN9	5780	broad.mit.edu	37	15	75766070	75766070	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75766070C>A	uc002bal.2	-	c.1168G>T	c.(1168-1170)GTA>TTA	p.V390L		NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type	390	Tyrosine-protein phosphatase.					cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2														0.141129	52.219119	82.991961	35	213	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75766070	75766070	13251	15	C	A	A	A	234	18	PTPN9	2	2
C15orf42	90381	broad.mit.edu	37	15	90128938	90128938	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:90128938G>T	uc002boe.2	+	c.1177_splice	c.e4-1	p.V393_splice		NM_152259	NP_689472			leucine-rich repeat kinase 1						cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|response to ionizing radiation|S-M checkpoint	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)	6	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)											0.123288	8.542267	18.666341	9	64	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	90128938	90128938	1846	15	G	T	T	T	455	35	C15orf42	5	2
C15orf32	145858	broad.mit.edu	37	15	93015490	93015490	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:93015490G>T	uc002brc.1	+	c.112G>T	c.(112-114)GGA>TGA	p.G38*	C15orf32_uc010bod.1_Non-coding_Transcript	NM_153040	NP_694585	Q32M92	CO032_HUMAN	hypothetical protein LOC145858	38										ovary(1)	1	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0493)|OV - Ovarian serous cystadenocarcinoma(32;0.125)											0.123596	22.213142	46.899897	22	156	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	93015490	93015490	1840	15	G	T	T	T	455	35	C15orf32	5	2
C16orf63	123811	broad.mit.edu	37	16	15967411	15967411	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:15967411C>A	uc002dec.1	-	c.385G>T	c.(385-387)GGG>TGG	p.G129W	C16orf63_uc002ded.1_Intron	NM_144600	NP_653201	Q96NB1	FOPNL_HUMAN	hypothetical protein LOC123811	129					cilium assembly|microtubule anchoring	centriolar satellite|microtubule basal body|motile cilium					0														0.175676	45.260509	59.942722	26	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15967411	15967411	1879	16	C	A	A	A	312	24	C16orf63	2	2
KIAA0556	23247	broad.mit.edu	37	16	27784480	27784480	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27784480G>T	uc002dow.2	+	c.4259G>T	c.(4258-4260)GGC>GTC	p.G1420V		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1420										ovary(4)|large_intestine(2)	6														0.28	35.328697	37.504839	14	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27784480	27784480	8490	16	G	T	T	T	546	42	KIAA0556	2	2
SBK1	388228	broad.mit.edu	37	16	28331646	28331646	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28331646G>T	uc002dpd.2	+	c.679G>T	c.(679-681)GGG>TGG	p.G227W		NM_001024401	NP_001019572	Q52WX2	SBK1_HUMAN	SH3-binding kinase 1	227	Protein kinase.					cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2										82				0.129032	4.479331	8.63427	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28331646	28331646	14341	16	G	T	T	T	507	39	SBK1	1	1
ITGAX	3687	broad.mit.edu	37	16	31384649	31384649	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31384649G>T	uc002ebt.2	+	c.2446G>T	c.(2446-2448)GGA>TGA	p.G816*	ITGAX_uc002ebu.1_Nonsense_Mutation_p.G816*	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	816	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.148325	47.400926	72.211447	31	178	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31384649	31384649	8193	16	G	T	T	T	507	39	ITGAX	5	1
ITGAX	3687	broad.mit.edu	37	16	31391186	31391186	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31391186G>T	uc002ebt.2	+	c.2976_splice	c.e25+1	p.Q992_splice	ITGAX_uc002ebu.1_Splice_Site_SNP_p.Q992_splice	NM_000887	NP_000878			integrin alpha X precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.153846	18.407756	25.855162	10	55	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	31391186	31391186	8193	16	G	T	T	T	572	44	ITGAX	5	2
ITGAD	3681	broad.mit.edu	37	16	31424230	31424230	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31424230C>A	uc010cap.1	+	c.1782C>A	c.(1780-1782)CTC>CTA	p.L594L	ITGAD_uc002ebv.1_Silent_p.L593L	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	593	Potential.|Extracellular (Potential).|FG-GAP 7.				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1														0.216561	67.05157	78.701374	34	123	KEEP	---	---	---	---	capture		Silent	SNP	31424230	31424230	8188	16	C	A	A	A	366	29	ITGAD	2	2
ITGAD	3681	broad.mit.edu	37	16	31429491	31429491	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31429491C>A	uc010cap.1	+	c.2598C>A	c.(2596-2598)CCC>CCA	p.P866P	ITGAD_uc002ebv.1_Silent_p.P865P	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	865	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1														0.142857	45.552171	74.881526	34	204	KEEP	---	---	---	---	capture		Silent	SNP	31429491	31429491	8188	16	C	A	A	A	262	21	ITGAD	2	2
CHD9	80205	broad.mit.edu	37	16	53330938	53330938	+	Nonsense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:53330938A>T	uc002ehb.2	+	c.5581A>T	c.(5581-5583)AGA>TGA	p.R1861*	CHD9_uc002egy.2_Nonsense_Mutation_p.R1861*|CHD9_uc002ehc.2_Nonsense_Mutation_p.R1861*|CHD9_uc002ehf.2_Nonsense_Mutation_p.R975*|CHD9_uc010cbw.2_Nonsense_Mutation_p.R229*	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1861					cellular lipid metabolic process|chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleoplasm	ATP binding|chromatin binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)								1157				0.242236	96.651728	106.402632	39	122	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	53330938	53330938	3466	16	A	T	T	T	88	7	CHD9	5	3
DPEP2	64174	broad.mit.edu	37	16	68021439	68021439	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68021439G>T	uc002evd.3	-	c.1446C>A	c.(1444-1446)GCC>GCA	p.A482A	DPEP2_uc010cey.2_Silent_p.A477A|DPEP2_uc002eve.2_Silent_p.A477A|DPEP2_uc002evf.2_Non-coding_Transcript	NM_022355	NP_071750	Q9H4A9	DPEP2_HUMAN	dipeptidase 2 precursor	477					hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis	anchored to membrane|plasma membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)										0.195055	130.985206	162.594514	71	293	KEEP	---	---	---	---	capture		Silent	SNP	68021439	68021439	4898	16	G	T	T	T	600	47	DPEP2	2	2
VAC14	55697	broad.mit.edu	37	16	70765433	70765433	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70765433C>T	uc002ezm.2	-	c.1626G>A	c.(1624-1626)CGG>CGA	p.R542R	VAC14_uc010cfw.2_Silent_p.R308R|VAC14_uc002ezn.2_Silent_p.R107R|VAC14_uc002ezl.2_5'UTR|VAC14_uc010cfx.1_Silent_p.R20R	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog	542					interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)	1		Ovarian(137;0.0699)												0.040609	-30.814066	13.90921	8	189	KEEP	---	---	---	---	capture		Silent	SNP	70765433	70765433	17676	16	C	T	T	T	379	30	VAC14	2	2
HYDIN	54768	broad.mit.edu	37	16	70841870	70841870	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70841870G>T	uc002ezr.2	-	c.14976C>A	c.(14974-14976)CCC>CCA	p.P4992P	HYDIN_uc010cfy.2_Non-coding_Transcript	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4993										ovary(1)	1		Ovarian(137;0.0654)												0.104167	7.110797	29.580932	15	129	KEEP	---	---	---	---	capture		Silent	SNP	70841870	70841870	7767	16	G	T	T	T	600	47	HYDIN	2	2
MYH13	8735	broad.mit.edu	37	17	10204269	10204269	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10204269C>T	uc002gmk.1	-	c.5816G>A	c.(5815-5817)TGA>TAA	p.*1939*		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1939					muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.088435	-0.25117	24.947023	13	134	KEEP	---	---	---	---	capture		Silent	SNP	10204269	10204269	10427	17	C	T	T	T	376	29	MYH13	2	2
MYH13	8735	broad.mit.edu	37	17	10222113	10222113	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10222113C>G	uc002gmk.1	-	c.3732G>C	c.(3730-3732)AAG>AAC	p.K1244N		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1244	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.116667	24.465049	41.809264	14	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10222113	10222113	10427	17	C	G	G	G	259	20	MYH13	3	3
MYH1	4619	broad.mit.edu	37	17	10408755	10408756	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10408755_10408756GG>TT	uc002gmo.2	-	c.2247_2248CC>AA	c.(2245-2250)CTCCTG>CTAATG	p.L750M		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	750	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.111111	21.00788	42.525008	16	128	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	10408755	10408756	10424	17	GG	TT	TT	TT	451	35	MYH1	2	2
MYH2	4620	broad.mit.edu	37	17	10426485	10426485	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10426485C>A	uc010coi.2	-	c.5595G>T	c.(5593-5595)AAG>AAT	p.K1865N	MYH2_uc002gmp.3_Missense_Mutation_p.K1865N|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1865	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.071429	-4.623417	11.285244	6	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10426485	10426485	10430	17	C	A	A	A	415	32	MYH2	2	2
MYH2	4620	broad.mit.edu	37	17	10428361	10428361	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10428361C>A	uc010coi.2	-	c.4684G>T	c.(4684-4686)GGA>TGA	p.G1562*	MYH2_uc002gmp.3_Nonsense_Mutation_p.G1562*|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1562	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.144385	31.779333	54.586564	27	160	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10428361	10428361	10430	17	C	A	A	A	286	22	MYH2	5	2
DNAH9	1770	broad.mit.edu	37	17	11514989	11514989	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11514989T>C	uc002gne.2	+	c.796T>C	c.(796-798)TAT>CAT	p.Y266H	DNAH9_uc002gnd.1_Missense_Mutation_p.Y266H	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	266	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.174825	64.297836	78.551282	25	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11514989	11514989	4791	17	T	C	C	C	689	53	DNAH9	4	4
DNAH9	1770	broad.mit.edu	37	17	11520764	11520764	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11520764T>C	uc002gne.2	+	c.941T>C	c.(940-942)ATA>ACA	p.I314T		NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	314	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.164706	33.30456	42.368029	14	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11520764	11520764	4791	17	T	C	C	C	637	49	DNAH9	4	4
MYOCD	93649	broad.mit.edu	37	17	12647645	12647645	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:12647645G>C	uc002gno.2	+	c.863G>C	c.(862-864)CGG>CCG	p.R288P	MYOCD_uc002gnn.2_Missense_Mutation_p.R288P|MYOCD_uc002gnp.1_Missense_Mutation_p.R192P|MYOCD_uc002gnq.2_Missense_Mutation_p.R7P	NM_001146312	NP_001139784	Q8IZQ8	MYCD_HUMAN	myocardin isoform 1	288					cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)										0.173469	33.712115	43.580384	17	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12647645	12647645	10482	17	G	C	C	C	507	39	MYOCD	3	3
MYO1C	4641	broad.mit.edu	37	17	1385813	1385813	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:1385813T>A	uc002fsp.2	-	c.586A>T	c.(586-588)AGC>TGC	p.S196C	MYO1C_uc002fsn.2_Missense_Mutation_p.S177C|MYO1C_uc002fso.2_Missense_Mutation_p.S161C|MYO1C_uc010vqj.1_Missense_Mutation_p.S161C|MYO1C_uc010vqk.1_Missense_Mutation_p.S172C	NM_001080779	NP_001074248	O00159	MYO1C_HUMAN	myosin IC isoform a	196	Myosin head-like.				mRNA transport|protein transport|transmembrane transport	basal plasma membrane|cytoplasm|filamentous actin|lateral plasma membrane|nuclear pore|nucleolus|nucleoplasm|stereocilium membrane	actin binding|ATP binding|calmodulin binding|motor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)										0.197368	34.684582	41.164735	15	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1385813	1385813	10465	17	T	A	A	A	715	55	MYO1C	3	3
NUFIP2	57532	broad.mit.edu	37	17	27614038	27614038	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:27614038G>A	uc002hdy.3	-	c.974C>T	c.(973-975)TCA>TTA	p.S325L	NUFIP2_uc002hdx.3_Intron	NM_020772	NP_065823	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein	325						nucleus|polysomal ribosome	protein binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)											0.120301	28.31293	66.182737	32	234	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27614038	27614038	11154	17	G	A	A	A	585	45	NUFIP2	2	2
PEX12	5193	broad.mit.edu	37	17	33904575	33904575	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33904575G>T	uc002hjp.2	-	c.162C>A	c.(160-162)TTC>TTA	p.F54L		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	54	Cytoplasmic (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.16996	67.164862	93.260493	43	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33904575	33904575	12162	17	G	T	T	T	425	33	PEX12	2	2
C17orf66	256957	broad.mit.edu	37	17	34192287	34192287	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34192287G>T	uc002hke.1	-	c.252C>A	c.(250-252)CAC>CAA	p.H84Q	C17orf66_uc010wck.1_Non-coding_Transcript|C17orf66_uc010wcl.1_Missense_Mutation_p.H84Q|C17orf66_uc010wcm.1_Missense_Mutation_p.H50Q	NM_152781	NP_689994	A2RTY3	CQ066_HUMAN	hypothetical protein LOC256957	84							binding			breast(2)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)										0.085366	2.771901	17.056888	7	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34192287	34192287	1931	17	G	T	T	T	516	40	C17orf66	1	1
CCL14	6358	broad.mit.edu	37	17	34310883	34310883	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34310883C>A	uc010wcq.1	-	c.284G>T	c.(283-285)AGT>ATT	p.S95I	CCL16_uc002hkl.2_5'Flank|CCL16_uc002hkm.2_5'Flank|CCL14_uc010wcr.1_Missense_Mutation_p.S79I|CCL14_uc002hkn.2_Non-coding_Transcript|CCL14-CCL15_uc010wcs.1_Non-coding_Transcript|CCL14-CCL15_uc010wct.1_Non-coding_Transcript	NM_032962	NP_116738	Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14 isoform 2	79					cellular calcium ion homeostasis|immune response|positive regulation of cell proliferation	extracellular space	chemokine activity|signal transducer activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.16129	35.35636	48.86988	20	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34310883	34310883	3010	17	C	A	A	A	260	20	CCL14	2	2
ERBB2	2064	broad.mit.edu	37	17	37864639	37864639	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:37864639G>A	uc002hso.2	+	c.291G>A	c.(289-291)CAG>CAA	p.Q97Q	ERBB2_uc002hsm.2_Silent_p.Q67Q|ERBB2_uc010cwa.2_Silent_p.Q82Q|ERBB2_uc002hsp.2_5'UTR|ERBB2_uc010cwb.2_Silent_p.Q97Q|ERBB2_uc010wek.1_Intron|ERBB2_uc002hsl.2_Silent_p.Q67Q|ERBB2_uc002hsn.1_Silent_p.Q97Q	NM_004448	NP_004439	P04626	ERBB2_HUMAN	erbB-2 isoform a	97	Extracellular (Potential).				cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(71)|central_nervous_system(16)|ovary(13)|stomach(12)|breast(5)|upper_aerodigestive_tract(4)|large_intestine(3)|liver(3)|endometrium(2)|pancreas(1)	130	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)			1		271	TCGA GBM(5;<1E-8)			0.122905	29.537337	54.438147	22	157	KEEP	---	---	---	---	capture		Silent	SNP	37864639	37864639	5399	17	G	A	A	A	425	33	ERBB2	2	2
GHDC	84514	broad.mit.edu	37	17	40344425	40344425	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40344425C>T	uc002hzd.2	-	c.723G>A	c.(721-723)CGG>CGA	p.R241R	GHDC_uc002hzg.1_Silent_p.R241R|GHDC_uc010wgg.1_Silent_p.R202R|GHDC_uc002hze.3_Silent_p.R241R|GHDC_uc002hzf.3_Silent_p.R241R|GHDC_uc010cxz.2_Non-coding_Transcript	NM_032484	NP_115873	Q8N2G8	GHDC_HUMAN	LGP1 homolog isoform 1	241						endoplasmic reticulum|nuclear envelope					0		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)										0.103825	14.498077	43.083148	19	164	KEEP	---	---	---	---	capture		Silent	SNP	40344425	40344425	6637	17	C	T	T	T	275	22	GHDC	2	2
AOC3	8639	broad.mit.edu	37	17	41003966	41003966	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41003966G>T	uc002ibv.2	+	c.606G>T	c.(604-606)AAG>AAT	p.K202N		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	202	Extracellular (Potential).				amine metabolic process|cell adhesion|inflammatory response|oxidation-reduction process	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)	3		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	NSCLC(3;192 220 10664 11501 16477)								0.141304	15.402687	26.859243	13	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41003966	41003966	738	17	G	T	T	T	438	34	AOC3	2	2
KPNB1	3837	broad.mit.edu	37	17	45755523	45755523	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:45755523C>G	uc002ilt.1	+	c.2215C>G	c.(2215-2217)CTT>GTT	p.L739V	KPNB1_uc010wkw.1_Missense_Mutation_p.L594V|KPNB1_uc010wkx.1_Missense_Mutation_p.L523V	NM_002265	NP_002256	Q14974	IMB1_HUMAN	karyopherin beta 1	739					DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)	2														0.106122	35.860898	73.615164	26	219	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45755523	45755523	8750	17	C	G	G	G	416	32	KPNB1	3	3
SGCA	6442	broad.mit.edu	37	17	48245036	48245036	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:48245036A>T	uc002iqi.2	+	c.251A>T	c.(250-252)CAC>CTC	p.H84L	SGCA_uc010wmh.1_Intron|SGCA_uc002iqj.2_Missense_Mutation_p.H84L|SGCA_uc010wmi.1_Non-coding_Transcript	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	84	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2														0.178571	28.326864	36.458342	15	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48245036	48245036	14690	17	A	T	T	T	78	6	SGCA	3	3
MMD	23531	broad.mit.edu	37	17	53491543	53491543	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:53491543T>C	uc002iui.2	-	c.77A>G	c.(76-78)TAT>TGT	p.Y26C		NM_012329	NP_036461	Q15546	PAQRB_HUMAN	monocyte to macrophage	26	Cytoplasmic (Potential).				cytolysis	integral to plasma membrane|late endosome membrane|lysosomal membrane|membrane fraction	receptor activity				0														0.054264	-9.171948	17.829742	7	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53491543	53491543	10033	17	T	C	C	C	637	49	MMD	4	4
ANKFN1	162282	broad.mit.edu	37	17	54543774	54543774	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:54543774C>G	uc002iun.1	+	c.1624C>G	c.(1624-1626)CAT>GAT	p.H542D		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	542										large_intestine(1)|ovary(1)	2														0.090909	15.519054	47.083631	17	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54543774	54543774	628	17	C	G	G	G	221	17	ANKFN1	3	3
AKAP1	8165	broad.mit.edu	37	17	55184111	55184111	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:55184111C>T	uc002iux.2	+	c.1286C>T	c.(1285-1287)TCA>TTA	p.S429L	AKAP1_uc010wnl.1_Missense_Mutation_p.S429L|AKAP1_uc002iuy.2_Non-coding_Transcript|AKAP1_uc010dcm.2_Missense_Mutation_p.S429L	NM_003488	NP_003479	Q92667	AKAP1_HUMAN	A-kinase anchor protein 1 precursor	429					blood coagulation	cytosol|integral to membrane|mitochondrial outer membrane	protein binding|RNA binding			ovary(1)	1	Breast(9;5.46e-08)													0.130435	22.884321	44.266947	21	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55184111	55184111	448	17	C	T	T	T	377	29	AKAP1	2	2
USP32	84669	broad.mit.edu	37	17	58256678	58256678	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58256678C>A	uc002iyo.1	-	c.4753G>T	c.(4753-4755)GAC>TAC	p.D1585Y	USP32_uc002iyn.1_Missense_Mutation_p.D1255Y	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	1585					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			large_intestine(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)											0.25	102.781865	113.714079	48	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58256678	58256678	17627	17	C	A	A	A	416	32	USP32	2	2
MRC2	9902	broad.mit.edu	37	17	60754829	60754829	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60754829A>T	uc002jad.2	+	c.2034A>T	c.(2032-2034)AAA>AAT	p.K678N	MRC2_uc010ddq.1_Non-coding_Transcript	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	678	Extracellular (Potential).|C-type lectin 4.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.217391	10.363486	12.058139	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60754829	60754829	10150	17	A	T	T	T	24	2	MRC2	3	3
GNA13	10672	broad.mit.edu	37	17	63010527	63010527	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:63010527C>G	uc002jfc.2	-	c.982G>C	c.(982-984)GAA>CAA	p.E328Q	GNA13_uc010wqh.1_Missense_Mutation_p.E233Q	NM_006572	NP_006563	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein),	328					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase D activity|cellular component movement|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex|melanosome	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity|type 1 angiotensin receptor binding				0														0.08284	8.616558	38.519796	14	155	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63010527	63010527	6770	17	C	G	G	G	390	30	GNA13	3	3
WIPI1	55062	broad.mit.edu	37	17	66430737	66430737	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:66430737C>T	uc010dey.2	-	c.652G>A	c.(652-654)GAT>AAT	p.D218N	WIPI1_uc002jhd.3_Non-coding_Transcript|WIPI1_uc010wqo.1_Missense_Mutation_p.D136N|WIPI1_uc002jhe.3_Non-coding_Transcript	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting	218	WD 1.				macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0														0.073684	-5.358995	12.40356	7	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66430737	66430737	17944	17	C	T	T	T	377	29	WIPI1	2	2
ABCA6	23460	broad.mit.edu	37	17	67102211	67102211	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:67102211C>T	uc002jhw.1	-	c.2531G>A	c.(2530-2532)CGT>CAT	p.R844H	ABCA6_uc002jhx.1_Missense_Mutation_p.R297H	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	844					transport	integral to membrane	ATP binding|ATPase activity			large_intestine(2)|ovary(2)	4	Breast(10;5.65e-12)													0.066116	-10.552084	13.059125	8	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67102211	67102211	37	17	C	T	T	T	247	19	ABCA6	1	1
DNAI2	64446	broad.mit.edu	37	17	72297289	72297289	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:72297289G>A	uc002jkf.2	+	c.969G>A	c.(967-969)CTG>CTA	p.L323L	DNAI2_uc002jkg.2_Non-coding_Transcript|DNAI2_uc010dfp.2_Non-coding_Transcript	NM_023036	NP_075462	Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate polypeptide 2	323					cilium assembly	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	microtubule motor activity			ovary(2)|central_nervous_system(1)	3														0.25	220.297922	240.530392	89	267	KEEP	---	---	---	---	capture		Silent	SNP	72297289	72297289	4793	17	G	A	A	A	600	47	DNAI2	2	2
TP53	7157	broad.mit.edu	37	17	7577082	7577082	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577082C>A	uc002gim.2	-	c.856G>T	c.(856-858)GAA>TAA	p.E286*	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Nonsense_Mutation_p.E286*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.E154*|TP53_uc010cng.1_Nonsense_Mutation_p.E154*|TP53_uc002gii.1_Nonsense_Mutation_p.E154*|TP53_uc010cnh.1_Nonsense_Mutation_p.E286*|TP53_uc010cni.1_Nonsense_Mutation_p.E286*|TP53_uc002gij.2_Nonsense_Mutation_p.E286*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	286	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		E -> V (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> G (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).|E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.E286K(48)|p.E286*(14)|p.0?(6)|p.E286Q(5)|p.?(2)|p.E286fs*59(2)|p.E286fs*17(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.G279fs*59(1)|p.R283fs*59(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	p.EE286del(CAL78-Tumor)|p.TEE284del(HCC1833-Tumor)|p.E286K(LP1-Tumor)|p.E286K(M059K-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.185185	24.375919	31.908611	15	66	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	7577082	7577082	16923	17	C	A	A	A	390	30	TP53	5	2
DNAH2	146754	broad.mit.edu	37	17	7734558	7734558	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7734558C>G	uc002giu.1	+	c.12385C>G	c.(12385-12387)CTC>GTC	p.L4129V	DNAH2_uc010cnm.1_Missense_Mutation_p.L1067V	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	4129	TPR 5.				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.068681	-12.024865	58.034273	25	339	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7734558	7734558	4785	17	C	G	G	G	312	24	DNAH2	3	3
TBC1D16	125058	broad.mit.edu	37	17	77925310	77925310	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77925310T>A	uc002jxj.2	-	c.1028A>T	c.(1027-1029)GAC>GTC	p.D343V	TBC1D16_uc002jxh.2_5'Flank|TBC1D16_uc002jxi.2_5'Flank|TBC1D16_uc002jxk.1_5'Flank	NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	343						intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			Ovarian(14;397 562 4850 31922 49378)								0.156627	39.843559	58.545944	26	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77925310	77925310	16127	17	T	A	A	A	754	58	TBC1D16	3	3
CCDC57	284001	broad.mit.edu	37	17	80151915	80151915	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:80151915C>A	uc002kdx.1	-	c.719G>T	c.(718-720)AGG>ATG	p.R240M	CCDC57_uc002kdz.1_Missense_Mutation_p.R240M	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	240	Potential.									ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)											0.24	47.949695	54.123792	24	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80151915	80151915	2950	17	C	A	A	A	312	24	CCDC57	2	2
CSNK1D	1453	broad.mit.edu	37	17	80223565	80223565	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:80223565C>T	uc002kef.2	-	c.184G>A	c.(184-186)GGA>AGA	p.G62R	CSNK1D_uc002kei.2_Missense_Mutation_p.G62R|CSNK1D_uc002kej.2_Missense_Mutation_p.G62R|CSNK1D_uc010wvj.1_5'UTR	NM_001893	NP_001884	P48730	KC1D_HUMAN	casein kinase 1, delta isoform 1	62	Protein kinase.				circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			breast(2)	2	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)						p.G62R(HCC2935-Tumor)|p.G62R(OV56-Tumor)|p.G62R(HT115-Tumor)|p.G62R(OVISE-Tumor)	44				0.071429	-5.16338	31.894195	14	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80223565	80223565	4093	17	C	T	T	T	312	24	CSNK1D	2	2
ARHGEF15	22899	broad.mit.edu	37	17	8218585	8218585	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8218585G>A	uc002glc.2	+	c.1250G>A	c.(1249-1251)CGC>CAC	p.R417H	ARHGEF15_uc002gld.2_Missense_Mutation_p.R417H|ARHGEF15_uc010vuw.1_Missense_Mutation_p.R306H	NM_173728	NP_776089	O94989	ARHGF_HUMAN	Rho guanine exchange factor 15	417	DH.				negative regulation of synapse maturation|regulation of Rho protein signal transduction	dendrite|intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2														0.220339	25.239968	29.493559	13	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8218585	8218585	912	17	G	A	A	A	494	38	ARHGEF15	1	1
GLP2R	9340	broad.mit.edu	37	17	9792900	9792900	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9792900G>T	uc002gmd.1	+	c.1540G>T	c.(1540-1542)GGC>TGC	p.G514C		NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor	514	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				ovary(1)	1					Glucagon recombinant(DB00040)									0.229508	28.717486	32.811917	14	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9792900	9792900	6721	17	G	T	T	T	559	43	GLP2R	2	2
SPIRE1	56907	broad.mit.edu	37	18	12479746	12479746	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:12479746C>G	uc002kre.2	-	c.1356G>C	c.(1354-1356)AAG>AAC	p.K452N	SPIRE1_uc002krc.2_Non-coding_Transcript|SPIRE1_uc010wzw.1_Missense_Mutation_p.K318N|SPIRE1_uc010wzx.1_Missense_Mutation_p.K241N|SPIRE1_uc010wzy.1_Missense_Mutation_p.K438N	NM_001128626	NP_001122098	Q08AE8	SPIR1_HUMAN	spire homolog 1 isoform a	452						cytoskeleton|perinuclear region of cytoplasm	actin binding|zinc ion binding				0														0.151163	24.944999	34.9753	13	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12479746	12479746	15584	18	C	G	G	G	363	28	SPIRE1	3	3
DSC3	1825	broad.mit.edu	37	18	28604459	28604459	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28604459A>G	uc002kwj.3	-	c.631T>C	c.(631-633)TTG>CTG	p.L211L	DSC3_uc002kwi.3_Silent_p.L211L	NM_001941	NP_001932	Q14574	DSC3_HUMAN	desmocollin 3 isoform Dsc3a preproprotein	211	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(10;0.125)											0.073171	1.091809	16.443202	6	76	KEEP	---	---	---	---	capture		Silent	SNP	28604459	28604459	4951	18	A	G	G	G	24	2	DSC3	4	4
C18orf34	374864	broad.mit.edu	37	18	30791950	30791950	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:30791950C>G	uc010xbr.1	-	c.2148G>C	c.(2146-2148)GAG>GAC	p.E716D	C18orf34_uc010dme.1_Missense_Mutation_p.E230D|C18orf34_uc002kxn.2_Missense_Mutation_p.E716D|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Missense_Mutation_p.E678D|C18orf34_uc002kxp.2_Missense_Mutation_p.E716D	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	716										ovary(1)	1														0.144444	25.211144	36.167358	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30791950	30791950	1963	18	C	G	G	G	415	32	C18orf34	3	3
ASXL3	80816	broad.mit.edu	37	18	31319721	31319721	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:31319721G>T	uc010dmg.1	+	c.2353G>T	c.(2353-2355)GAG>TAG	p.E785*	ASXL3_uc002kxq.2_Nonsense_Mutation_p.E492*	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	785	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3														0.140351	8.25578	15.397034	8	49	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31319721	31319721	1087	18	G	T	T	T	585	45	ASXL3	5	2
FHOD3	80206	broad.mit.edu	37	18	34324149	34324149	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:34324149C>A	uc002kzs.1	+	c.3509C>A	c.(3508-3510)TCA>TAA	p.S1170*	FHOD3_uc002kzt.1_Nonsense_Mutation_p.S1153*|FHOD3_uc010dmz.1_Nonsense_Mutation_p.S885*|FHOD3_uc010dnb.1_Nonsense_Mutation_p.S149*	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1153	FH2.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			large_intestine(2)|breast(2)|ovary(1)	5		all_epithelial(2;0.0181)|Colorectal(2;0.0195)												0.098592	5.533581	28.440146	14	128	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	34324149	34324149	6121	18	C	A	A	A	377	29	FHOD3	5	2
KIAA1632	57724	broad.mit.edu	37	18	43497731	43497731	+	Nonsense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43497731G>C	uc002lbm.2	-	c.3152C>G	c.(3151-3153)TCA>TGA	p.S1051*	KIAA1632_uc002lbo.1_Nonsense_Mutation_p.S1051*|KIAA1632_uc010xcq.1_5'Flank|KIAA1632_uc010xcr.1_5'Flank|KIAA1632_uc010xcs.1_5'Flank|KIAA1632_uc002lbn.2_5'UTR	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	1051					autophagy						0														0.033708	-26.611244	15.570416	6	172	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	43497731	43497731	8558	18	G	C	C	C	585	45	KIAA1632	5	3
CDH20	28316	broad.mit.edu	37	18	59166451	59166451	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59166451C>A	uc010dps.1	+	c.279C>A	c.(277-279)TCC>TCA	p.S93S	CDH20_uc002lif.2_Silent_p.S87S	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	93	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)												0.090909	-1.421343	9.797676	6	60	KEEP	---	---	---	---	capture		Silent	SNP	59166451	59166451	3235	18	C	A	A	A	262	21	CDH20	2	2
SERPINB4	6318	broad.mit.edu	37	18	61324130	61324130	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61324130G>A	uc002ljg.2	-	c.703C>T	c.(703-705)CCA>TCA	p.P235S	SERPINB3_uc002lji.2_Missense_Mutation_p.P235S|SERPINB3_uc010dqa.2_Intron	SERPINB4		P48594	SPB4_HUMAN	SubName: Full=Squamous cell carcinoma antigen 2;	235					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity	p.L232_Y236>H(1)		ovary(1)|lung(1)	2										163				0.057895	-18.440697	20.523056	11	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61324130	61324130	14591	18	G	A	A	A	572	44	SERPINB4	2	2
SERPINB8	5271	broad.mit.edu	37	18	61654176	61654176	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61654176G>T	uc002ljv.2	+	c.789G>T	c.(787-789)AAG>AAT	p.K263N	SERPINB8_uc002lju.2_Missense_Mutation_p.K263N|SERPINB8_uc010xex.1_Missense_Mutation_p.K81N	NM_198833	NP_942130	P50452	SPB8_HUMAN	serine (or cysteine) proteinase inhibitor, clade	263					regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)												0.15528	35.573563	53.8576	25	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61654176	61654176	14595	18	G	T	T	T	451	35	SERPINB8	2	2
CDH7	1005	broad.mit.edu	37	18	63547963	63547963	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:63547963C>A	uc002ljz.2	+	c.2191C>A	c.(2191-2193)CAG>AAG	p.Q731K	CDH7_uc002lkb.2_Missense_Mutation_p.Q731K	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	731	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.129)												0.181818	62.07557	78.839622	32	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63547963	63547963	3244	18	C	A	A	A	325	25	CDH7	2	2
LAMA1	284217	broad.mit.edu	37	18	6943380	6943380	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:6943380C>A	uc002knm.2	-	c.8866G>T	c.(8866-8868)GGT>TGT	p.G2956C	LAMA1_uc002knk.2_Missense_Mutation_p.G286C|LAMA1_uc002knl.2_Missense_Mutation_p.G409C|LAMA1_uc010wzj.1_Missense_Mutation_p.G2432C	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2956	Laminin G-like 5.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.1	9.703104	38.489878	18	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6943380	6943380	8928	18	C	A	A	A	273	21	LAMA1	2	2
CYP4F2	8529	broad.mit.edu	37	19	16003139	16003139	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:16003139C>G	uc002nbs.1	-	c.505G>C	c.(505-507)GAG>CAG	p.E169Q	CYP4F2_uc010xot.1_Missense_Mutation_p.E20Q|CYP4F2_uc010xou.1_Missense_Mutation_p.E20Q	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,	169				E -> D (in Ref. 7; AAH67440).	leukotriene metabolic process|long-chain fatty acid metabolic process|oxidation-reduction process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2														0.127551	52.231722	78.739259	25	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16003139	16003139	4353	19	C	G	G	G	377	29	CYP4F2	3	3
FAM129C	199786	broad.mit.edu	37	19	17664237	17664237	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17664237T>C	uc010xpr.1	+	c.1959T>C	c.(1957-1959)TCT>TCC	p.S653S	GLT25D1_uc002nhc.1_5'Flank	NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a	653											0														0.129032	47.270281	72.192547	24	162	KEEP	---	---	---	---	capture		Silent	SNP	17664237	17664237	5635	19	T	C	C	C	717	56	FAM129C	4	4
CRLF1	9244	broad.mit.edu	37	19	18710582	18710582	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18710582C>T	uc010ebt.1	-	c.190G>A	c.(190-192)GGA>AGA	p.G64R		NM_004750	NP_004741	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1 precursor	64	Ig-like C2-type.				negative regulation of neuron apoptosis|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	cytokine binding|protein heterodimerization activity|receptor activity			central_nervous_system(1)	1														0.230769	5.618802	6.48258	3	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18710582	18710582	4025	19	C	T	T	T	299	23	CRLF1	1	1
DDX49	54555	broad.mit.edu	37	19	19033223	19033223	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19033223G>A	uc002nkq.1	+	c.536G>A	c.(535-537)CGC>CAC	p.R179H	HOMER3_uc002nko.1_Intron|HOMER3_uc002nkp.1_Intron|DDX49_uc002nkr.1_Non-coding_Transcript|DDX49_uc002nks.1_Missense_Mutation_p.R72H|DDX49_uc002nkt.1_Missense_Mutation_p.R61H	NM_019070	NP_061943	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	179	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			Epithelial(12;0.0289)											0.304348	16.217799	17.002684	7	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19033223	19033223	4537	19	G	A	A	A	494	38	DDX49	1	1
GMIP	51291	broad.mit.edu	37	19	19749278	19749278	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19749278T>A	uc002nnd.2	-	c.551A>T	c.(550-552)AAA>ATA	p.K184I	GMIP_uc010xrb.1_Missense_Mutation_p.K184I|GMIP_uc010xrc.1_Missense_Mutation_p.K184I	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	184					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1														0.186047	13.67151	17.648129	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19749278	19749278	6760	19	T	A	A	A	832	64	GMIP	3	3
ZNF536	9745	broad.mit.edu	37	19	30936620	30936620	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30936620C>A	uc002nsu.1	+	c.2151C>A	c.(2149-2151)CCC>CCA	p.P717P	ZNF536_uc010edd.1_Silent_p.P717P	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	717					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.185185	17.316217	22.337872	10	44	KEEP	---	---	---	---	capture		Silent	SNP	30936620	30936620	18568	19	C	A	A	A	301	24	ZNF536	2	2
C19orf40	91442	broad.mit.edu	37	19	33464996	33464996	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:33464996G>C	uc002nud.3	+	c.274G>C	c.(274-276)GAA>CAA	p.E92Q	CCDC123_uc002nty.2_5'Flank|CCDC123_uc010edg.2_5'Flank|CCDC123_uc002ntz.1_5'Flank|CCDC123_uc002nua.2_5'Flank|CCDC123_uc002nuc.1_5'Flank	NM_152266	NP_689479	Q9BTP7	FAP24_HUMAN	Fanconi anemia-associated protein, 24 kDa	92					DNA repair	Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding				0	Esophageal squamous(110;0.137)													0.133333	24.233945	35.978761	12	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33464996	33464996	1987	19	G	C	C	C	585	45	C19orf40	3	3
MAG	4099	broad.mit.edu	37	19	35790577	35790577	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35790577G>A	uc002nyy.1	+	c.536G>A	c.(535-537)GGG>GAG	p.G179E	MAG_uc002nyx.1_Missense_Mutation_p.G179E|MAG_uc010eds.1_Missense_Mutation_p.G154E|MAG_uc002nyz.1_Missense_Mutation_p.G179E	NM_002361	NP_002352	P20916	MAG_HUMAN	myelin associated glycoprotein isoform a	179	Ig-like C2-type 1.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane	sugar binding			central_nervous_system(1)	1	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)											0.130435	4.410032	7.46482	3	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35790577	35790577	9539	19	G	A	A	A	559	43	MAG	2	2
HCST	10870	broad.mit.edu	37	19	36393498	36393498	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36393498G>T	uc002ocl.1	+	c.3G>T	c.(1-3)ATG>ATT	p.M1I	NFKBID_uc002oci.1_5'Flank|NFKBID_uc002ocj.1_5'Flank|HCST_uc002ock.1_Missense_Mutation_p.M1I	NM_014266	NP_055081	Q9UBK5	HCST_HUMAN	hematopoietic cell signal transducer isoform 1	1					regulation of immune response	integral to membrane|plasma membrane					0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.111919	58.324036	160.81455	77	611	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36393498	36393498	7286	19	G	T	T	T	585	45	HCST	2	2
ZNF780A	284323	broad.mit.edu	37	19	40587733	40587735	+	Missense_Mutation	TNP	CCG	AAA	AAA			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40587733_40587735CCG>AAA	uc010xvh.1	-	c.226_228CGG>TTT	c.(226-228)CGG>TTT	p.R76F	ZNF780A_uc002omw.3_Missense_Mutation_p.R91F|ZNF780A_uc002omy.2_Missense_Mutation_p.R75F|ZNF780A_uc002omz.2_Missense_Mutation_p.R75F	NM_001142577	NP_001136049	O75290	Z780A_HUMAN	zinc finger protein 780A isoform a	75	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)													0.079365	-2.036297	20.719388	10	116	KEEP	---	---	---	---	capture		Missense_Mutation	TNP	40587733	40587735	18750	19	CCG	AAA	AAA	AAA	223	18	ZNF780A	2	2
RSPH6A	81492	broad.mit.edu	37	19	46303752	46303752	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46303752A>G	uc002pdm.2	-	c.1868T>C	c.(1867-1869)GTT>GCT	p.V623A	RSPH6A_uc002pdl.2_Missense_Mutation_p.V359A	NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1	623	Glu-rich.					intracellular				ovary(1)|central_nervous_system(1)	2														0.129032	13.671679	21.967467	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46303752	46303752	14187	19	A	G	G	G	26	2	RSPH6A	4	4
PRMT1	3276	broad.mit.edu	37	19	50188237	50188237	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50188237G>A	uc010enf.1	+	c.702G>A	c.(700-702)GAG>GAA	p.E234E	PRMT1_uc002ppc.1_Non-coding_Transcript|PRMT1_uc002ppd.2_Silent_p.E210E|PRMT1_uc002ppe.2_Silent_p.E216E|PRMT1_uc002ppf.2_Non-coding_Transcript|PRMT1_uc002ppg.2_Silent_p.E181E|PRMT1_uc010yba.1_Non-coding_Transcript|PRMT1_uc010ybb.1_5'Flank	NM_001536	NP_001527	Q99873	ANM1_HUMAN	HMT1 hnRNP methyltransferase-like 2 isoform 1	224					cell surface receptor linked signaling pathway|neuron projection development	cytosol|nucleus	histone methyltransferase activity (H4-R3 specific)|protein binding			ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)								OREG0025627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.170732	23.148637	31.522662	14	68	KEEP	---	---	---	---	capture		Silent	SNP	50188237	50188237	12978	19	G	A	A	A	438	34	PRMT1	2	2
NLRP2	55655	broad.mit.edu	37	19	55508760	55508760	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55508760C>T	uc002qij.2	+	c.2955C>T	c.(2953-2955)GTC>GTT	p.V985V	NLRP2_uc010yfp.1_Silent_p.V962V|NLRP2_uc010esn.2_Silent_p.V961V|NLRP2_uc010eso.2_Silent_p.V982V|NLRP2_uc010esp.2_Silent_p.V963V	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	985	LRR 7.				apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)										0.2	91.805926	111.072563	46	184	KEEP	---	---	---	---	capture		Silent	SNP	55508760	55508760	10880	19	C	T	T	T	366	29	NLRP2	2	2
PEG3	5178	broad.mit.edu	37	19	57327996	57327996	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57327996C>A	uc002qnu.2	-	c.1814G>T	c.(1813-1815)GGG>GTG	p.G605V	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Missense_Mutation_p.G576V|PEG3_uc002qnv.2_Missense_Mutation_p.G605V|PEG3_uc002qnw.2_Missense_Mutation_p.G481V|PEG3_uc002qnx.2_Missense_Mutation_p.G479V|PEG3_uc010etr.2_Missense_Mutation_p.G605V	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	605					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)										0.26	28.048723	30.659695	13	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57327996	57327996	12141	19	C	A	A	A	286	22	PEG3	2	2
EMR1	2015	broad.mit.edu	37	19	6897298	6897298	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6897298G>A	uc002mfw.2	+	c.377G>A	c.(376-378)GGC>GAC	p.G126D	EMR1_uc010dvc.2_Missense_Mutation_p.G126D|EMR1_uc010dvb.2_Intron|EMR1_uc010xji.1_Intron|EMR1_uc010xjj.1_Missense_Mutation_p.G126D	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	126	Extracellular (Potential).|EGF-like 2; calcium-binding (Potential).				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)	3	all_hematologic(4;0.166)													0.054545	-12.919765	10.085954	6	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6897298	6897298	5297	19	G	A	A	A	546	42	EMR1	2	2
MUC16	94025	broad.mit.edu	37	19	9024497	9024497	+	Splice_Site_SNP	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9024497C>A	uc002mkp.2	-	c.37037_splice	c.e17-1	p.G12346_splice		NM_024690	NP_078966			mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.153846	14.401251	21.85829	10	55	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	9024497	9024497	10367	19	C	A	A	A	312	24	MUC16	5	2
MUC16	94025	broad.mit.edu	37	19	9049935	9049935	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9049935C>G	uc002mkp.2	-	c.31696G>C	c.(31696-31698)GAG>CAG	p.E10566Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10568	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.152466	78.20827	103.987344	34	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9049935	9049935	10367	19	C	G	G	G	416	32	MUC16	3	3
MUC16	94025	broad.mit.edu	37	19	9057909	9057909	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9057909G>C	uc002mkp.2	-	c.29537C>G	c.(29536-29538)ACC>AGC	p.T9846S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	9848	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.107527	33.962969	62.374696	20	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9057909	9057909	10367	19	G	C	C	C	572	44	MUC16	3	3
MUC16	94025	broad.mit.edu	37	19	9075971	9075971	+	Silent	SNP	T	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9075971T>G	uc002mkp.2	-	c.11475A>C	c.(11473-11475)CCA>CCC	p.P3825P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3826	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.159544	100.272931	139.039459	56	295	KEEP	---	---	---	---	capture		Silent	SNP	9075971	9075971	10367	19	T	G	G	G	704	55	MUC16	4	4
NTNG1	22854	broad.mit.edu	37	1	107973450	107973450	+	Missense_Mutation	SNP	A	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:107973450A>C	uc001dvh.3	+	c.1166A>C	c.(1165-1167)CAC>CCC	p.H389P	NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvi.2_Intron|NTNG1_uc001dve.2_Non-coding_Transcript|NTNG1_uc009wek.2_Intron|NTNG1_uc001dvg.2_Intron|NTNG1_uc009wem.2_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1	389	Laminin EGF-like 2.				axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)	4		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)										0.095238	4.405519	14.762738	6	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107973450	107973450	11109	1	A	C	C	C	78	6	NTNG1	4	4
CELSR2	1952	broad.mit.edu	37	1	109812142	109812142	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109812142G>A	uc001dxa.3	+	c.6909G>A	c.(6907-6909)ACG>ACA	p.T2303T		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	2303	Extracellular (Potential).				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of gene-specific transcription|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)	3		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		NSCLC(158;1285 2011 34800 34852 42084)								0.186047	43.747606	55.649374	24	105	KEEP	---	---	---	---	capture		Silent	SNP	109812142	109812142	3355	1	G	A	A	A	496	39	CELSR2	1	1
SYPL2	284612	broad.mit.edu	37	1	110019410	110019410	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110019410C>A	uc001dxp.2	+	c.267C>A	c.(265-267)ATC>ATA	p.I89I	SYPL2_uc001dxo.2_Silent_p.I89I|SYPL2_uc010ovk.1_Silent_p.I89I|SYPL2_uc001dxq.2_5'UTR	NM_001040709	NP_001035799	Q5VXT5	SYPL2_HUMAN	mitsugumin 29	89	Vesicular (Potential).|MARVEL.					integral to membrane|synaptic vesicle	transporter activity			ovary(1)	1		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)										0.192982	19.489215	24.509653	11	46	KEEP	---	---	---	---	capture		Silent	SNP	110019410	110019410	15984	1	C	A	A	A	382	30	SYPL2	2	2
GPR61	83873	broad.mit.edu	37	1	110086511	110086511	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110086511C>A	uc001dxy.2	+	c.867C>A	c.(865-867)CTC>CTA	p.L289L		NM_031936	NP_114142	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	289	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(2)	2		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)										0.165517	36.300179	51.707474	24	121	KEEP	---	---	---	---	capture		Silent	SNP	110086511	110086511	6977	1	C	A	A	A	379	30	GPR61	2	2
RSBN1	54665	broad.mit.edu	37	1	114310969	114310969	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:114310969G>A	uc001edq.2	-	c.1701C>T	c.(1699-1701)ACC>ACT	p.T567T	RSBN1_uc001edr.2_Non-coding_Transcript	NM_018364	NP_060834	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	567						nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.105769	9.963734	26.009545	11	93	KEEP	---	---	---	---	capture		Silent	SNP	114310969	114310969	14176	1	G	A	A	A	600	47	RSBN1	2	2
CSDE1	7812	broad.mit.edu	37	1	115267878	115267878	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:115267878T>C	uc001efi.2	-	c.1855A>G	c.(1855-1857)AAA>GAA	p.K619E	CSDE1_uc001efj.2_Non-coding_Transcript|CSDE1_uc001efk.2_Missense_Mutation_p.K573E|CSDE1_uc001efl.2_Missense_Mutation_p.K542E|CSDE1_uc001efm.2_Missense_Mutation_p.K588E|CSDE1_uc009wgv.2_Missense_Mutation_p.K573E|CSDE1_uc001efn.2_Missense_Mutation_p.K542E	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1	573	CSD 7.				male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.052632	-20.243055	23.955856	11	198	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115267878	115267878	4070	1	T	C	C	C	819	63	CSDE1	4	4
FLG	2312	broad.mit.edu	37	1	152286758	152286758	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152286758C>A	uc001ezu.1	-	c.604G>T	c.(604-606)GAA>TAA	p.E202*		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	202	Potential.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.050955	-21.14238	12.430929	8	149	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	152286758	152286758	6160	1	C	A	A	A	377	29	FLG	5	2
LCE3E	353145	broad.mit.edu	37	1	152538599	152538599	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152538599C>A	uc001faa.2	-	c.86G>T	c.(85-87)TGT>TTT	p.C29F		NM_178435	NP_848522	Q5T5B0	LCE3E_HUMAN	late cornified envelope 3E	29					keratinization					ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		Lung(1;0.000294)|LUAD - Lung adenocarcinoma(1;0.00527)|LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)										0.226601	109.635374	123.573867	46	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152538599	152538599	8996	1	C	A	A	A	221	17	LCE3E	2	2
AQP10	89872	broad.mit.edu	37	1	154296762	154296762	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154296762G>A	uc001feu.2	+	c.712G>A	c.(712-714)GGT>AGT	p.G238S	AQP10_uc001fev.2_3'UTR|ATP8B2_uc001few.2_5'Flank	NM_080429	NP_536354	Q96PS8	AQP10_HUMAN	aquaporin 10	238	Extracellular (Potential).				response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)									OREG0013832	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.197183	28.908477	34.97428	14	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154296762	154296762	833	1	G	A	A	A	611	47	AQP10	2	2
ATP8B2	57198	broad.mit.edu	37	1	154319215	154319215	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154319215C>T	uc001fex.2	+	c.3243C>T	c.(3241-3243)CCC>CCT	p.P1081P		NM_020452	NP_065185	P98198	AT8B2_HUMAN	ATPase, class I, type 8B, member 2 isoform a	1067	Extracellular (Potential).				ATP biosynthetic process	plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)											0.194719	122.636349	148.988692	59	244	KEEP	---	---	---	---	capture		Silent	SNP	154319215	154319215	1214	1	C	T	T	T	262	21	ATP8B2	2	2
CD1E	913	broad.mit.edu	37	1	158325684	158325684	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158325684T>C	uc001fse.2	+	c.693T>C	c.(691-693)CAT>CAC	p.H231H	CD1E_uc010pid.1_Silent_p.H229H|CD1E_uc010pie.1_Silent_p.H132H|CD1E_uc010pif.1_Silent_p.H42H|CD1E_uc001fsd.2_Silent_p.H231H|CD1E_uc001fsk.2_Silent_p.H141H|CD1E_uc001fsj.2_Silent_p.H141H|CD1E_uc001fsc.2_Silent_p.H42H|CD1E_uc010pig.1_Non-coding_Transcript|CD1E_uc001fsa.2_Silent_p.H42H|CD1E_uc001fsf.2_Silent_p.H231H|CD1E_uc001fry.2_Silent_p.H231H|CD1E_uc001fsg.2_Silent_p.H42H|CD1E_uc001fsh.2_Silent_p.H42H|CD1E_uc001fsi.2_Silent_p.H231H|CD1E_uc009wsv.2_Silent_p.H132H|CD1E_uc001frz.2_Silent_p.H141H|CD1E_uc009wsw.2_5'UTR	NM_030893	NP_112155	P15812	CD1E_HUMAN	CD1E antigen isoform a precursor	231	Ig-like.				antigen processing and presentation|immune response	early endosome|Golgi membrane|integral to plasma membrane|late endosome|lysosomal lumen					0	all_hematologic(112;0.0378)													0.3	136.635914	142.357687	48	112	KEEP	---	---	---	---	capture		Silent	SNP	158325684	158325684	3105	1	T	C	C	C	660	51	CD1E	4	4
OR10X1	128367	broad.mit.edu	37	1	158548787	158548787	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158548787G>A	uc010pin.1	-	c.903C>T	c.(901-903)ATC>ATT	p.I301I		NM_001004477	NP_001004477	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X,	301	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.219136	146.078809	169.71224	71	253	KEEP	---	---	---	---	capture		Silent	SNP	158548787	158548787	11328	1	G	A	A	A	577	45	OR10X1	2	2
SPTA1	6708	broad.mit.edu	37	1	158583603	158583603	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158583603G>T	uc001fst.1	-	c.6897C>A	c.(6895-6897)TGC>TGA	p.C2299*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2299	EF-hand 1.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.097015	6.812185	28.583603	13	121	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	158583603	158583603	15630	1	G	T	T	T	542	42	SPTA1	5	2
IFI16	3428	broad.mit.edu	37	1	158988299	158988299	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158988299C>A	uc001ftg.2	+	c.830C>A	c.(829-831)TCT>TAT	p.S277Y	IFI16_uc010pis.1_Missense_Mutation_p.S221Y|IFI16_uc001ftf.1_Missense_Mutation_p.S277Y	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	277	HIN-200 1.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nucleolus|nucleoplasm	double-stranded DNA binding|transcription repressor activity			ovary(1)	1	all_hematologic(112;0.0429)													0.13913	21.014177	35.495703	16	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158988299	158988299	7812	1	C	A	A	A	416	32	IFI16	2	2
ADAMTS4	9507	broad.mit.edu	37	1	161165312	161165312	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161165312C>A	uc001fyt.3	-	c.1204G>T	c.(1204-1206)GAG>TAG	p.E402*		NM_005099	NP_005090	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1	402	Peptidase M12B.				proteolysis|skeletal system development	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|protease binding|zinc ion binding			ovary(4)|central_nervous_system(1)	5	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)											0.110092	19.885322	69.097921	36	291	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	161165312	161165312	269	1	C	A	A	A	390	30	ADAMTS4	5	2
C1orf226	400793	broad.mit.edu	37	1	162353098	162353098	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:162353098G>A	uc010pkt.1	+	c.573G>A	c.(571-573)CTG>CTA	p.L191L	C1orf226_uc001gby.2_Silent_p.L148L	NM_001135240	NP_001128712	A1L170	CA226_HUMAN	hypothetical protein LOC400793 isoform 1	148										ovary(1)	1														0.195122	15.97517	19.530718	8	33	KEEP	---	---	---	---	capture		Silent	SNP	162353098	162353098	2103	1	G	A	A	A	600	47	C1orf226	2	2
C1orf105	92346	broad.mit.edu	37	1	172437600	172437600	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:172437600T>A	uc001gik.2	+	c.418T>A	c.(418-420)TAC>AAC	p.Y140N		NM_139240	NP_640333	O95561	CA105_HUMAN	hypothetical protein LOC92346	140											0														0.096698	13.26491	82.400154	41	383	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172437600	172437600	2046	1	T	A	A	A	689	53	C1orf105	3	3
C1orf105	92346	broad.mit.edu	37	1	172437623	172437623	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:172437623C>A	uc001gik.2	+	c.441C>A	c.(439-441)CCC>CCA	p.P147P		NM_139240	NP_640333	O95561	CA105_HUMAN	hypothetical protein LOC92346	147											0														0.106339	32.718993	108.02248	52	437	KEEP	---	---	---	---	capture		Silent	SNP	172437623	172437623	2046	1	C	A	A	A	262	21	C1orf105	2	2
FAM5B	57795	broad.mit.edu	37	1	177250580	177250580	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:177250580G>T	uc001glf.2	+	c.2268G>T	c.(2266-2268)GTG>GTT	p.V756V	FAM5B_uc001glg.2_Silent_p.V651V	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	756						extracellular region				ovary(2)	2														0.129944	23.514406	47.131571	23	154	KEEP	---	---	---	---	capture		Silent	SNP	177250580	177250580	5816	1	G	T	T	T	600	47	FAM5B	2	2
NPHS2	7827	broad.mit.edu	37	1	179520370	179520370	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179520370G>T	uc001gmq.3	-	c.1090C>A	c.(1090-1092)CCA>ACA	p.P364T	C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmo.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron|NPHS2_uc009wxi.2_Missense_Mutation_p.P296T|C1orf125_uc001gmr.2_Non-coding_Transcript	NM_014625	NP_055440	Q9NP85	PODO_HUMAN	podocin	364	Cytoplasmic (Potential).				excretion	integral to plasma membrane	protein binding				0														0.1375	23.834636	44.19912	22	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179520370	179520370	10987	1	G	T	T	T	559	43	NPHS2	2	2
TDRD5	163589	broad.mit.edu	37	1	179621246	179621246	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179621246G>A	uc010pnp.1	+	c.2074G>A	c.(2074-2076)GAA>AAA	p.E692K	TDRD5_uc001gnf.1_Missense_Mutation_p.E692K|TDRD5_uc001gnh.1_Missense_Mutation_p.E247K	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	692					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.141844	32.502223	49.948743	20	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179621246	179621246	16260	1	G	A	A	A	429	33	TDRD5	2	2
FAM163A	148753	broad.mit.edu	37	1	179782940	179782940	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179782940C>A	uc009wxj.2	+	c.120C>A	c.(118-120)ACC>ACA	p.T40T	FAM163A_uc001gnj.2_Silent_p.T40T|FAM163A_uc009wxk.2_Silent_p.T40T	NM_173509	NP_775780	Q96GL9	F163A_HUMAN	hypothetical protein LOC148753	40						integral to membrane				ovary(1)	1														0.137097	21.108922	36.90367	17	107	KEEP	---	---	---	---	capture		Silent	SNP	179782940	179782940	5680	1	C	A	A	A	288	23	FAM163A	1	1
PAX7	5081	broad.mit.edu	37	1	18960982	18960982	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:18960982C>G	uc001bay.2	+	c.271C>G	c.(271-273)CAG>GAG	p.Q91E	PAX7_uc001baz.2_Missense_Mutation_p.Q91E|PAX7_uc010oct.1_Missense_Mutation_p.Q91E	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1	91	Paired.				anti-apoptosis|regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity		PAX7/FOXO1(197)	soft_tissue(197)|ovary(1)|lung(1)	199		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)						129				0.118421	11.418	22.291157	9	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18960982	18960982	11904	1	C	G	G	G	273	21	PAX7	3	3
KCNT2	343450	broad.mit.edu	37	1	196395118	196395118	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196395118C>A	uc001gtd.1	-	c.985G>T	c.(985-987)GAT>TAT	p.D329Y	KCNT2_uc009wyt.1_Non-coding_Transcript|KCNT2_uc001gte.1_Missense_Mutation_p.D329Y|KCNT2_uc001gtf.1_Missense_Mutation_p.D329Y|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Missense_Mutation_p.D329Y|KCNT2_uc009wyv.1_Missense_Mutation_p.D304Y	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	329	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|catalytic activity|voltage-gated potassium channel activity			ovary(4)|breast(1)	5														0.304348	81.415557	85.325782	35	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196395118	196395118	8397	1	C	A	A	A	390	30	KCNT2	2	2
PTPRC	5788	broad.mit.edu	37	1	198668802	198668802	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:198668802C>T	uc001gur.1	+	c.402C>T	c.(400-402)CTC>CTT	p.L134L	PTPRC_uc001gus.1_Silent_p.L134L|PTPRC_uc001gut.1_Intron|PTPRC_uc009wze.1_Silent_p.L70L|PTPRC_uc009wzf.1_Silent_p.L70L|PTPRC_uc010ppg.1_Silent_p.L70L|PTPRC_uc001guu.1_Silent_p.L177L|PTPRC_uc001guv.1_Non-coding_Transcript|PTPRC_uc001guw.1_Non-coding_Transcript	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	134	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815		OREG0014061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.084184	-7.334298	61.601876	33	359	KEEP	---	---	---	---	capture		Silent	SNP	198668802	198668802	13254	1	C	T	T	T	366	29	PTPRC	2	2
LRRN2	10446	broad.mit.edu	37	1	204588984	204588984	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204588984G>T	uc001hbe.1	-	c.137C>A	c.(136-138)TCC>TAC	p.S46Y	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Missense_Mutation_p.S46Y|LRRN2_uc009xbf.1_Missense_Mutation_p.S46Y|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	46	Extracellular (Potential).|LRRNT.				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)											0.101124	2.465771	16.556604	9	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204588984	204588984	9411	1	G	T	T	T	533	41	LRRN2	2	2
LGTN	1939	broad.mit.edu	37	1	206785640	206785640	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206785640C>A	uc001heh.2	-	c.56G>T	c.(55-57)AGG>ATG	p.R19M	LGTN_uc009xbw.2_Missense_Mutation_p.R19M|LGTN_uc010prw.1_Missense_Mutation_p.R19M	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin	19					intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)											0.253968	104.989324	115.396663	48	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206785640	206785640	9086	1	C	A	A	A	312	24	LGTN	2	2
USH2A	7399	broad.mit.edu	37	1	216062334	216062334	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216062334A>T	uc001hku.1	-	c.7657T>A	c.(7657-7659)TGG>AGG	p.W2553R		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2553	Fibronectin type-III 12.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.125628	25.537904	52.788754	25	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216062334	216062334	17598	1	A	T	T	T	91	7	USH2A	3	3
USH2A	7399	broad.mit.edu	37	1	216251604	216251604	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216251604C>G	uc001hku.1	-	c.5399G>C	c.(5398-5400)TGG>TCG	p.W1800S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1800	Laminin G-like 2.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.234513	390.000623	433.813486	159	519	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216251604	216251604	17598	1	C	G	G	G	273	21	USH2A	3	3
USH2A	7399	broad.mit.edu	37	1	216251649	216251649	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216251649G>C	uc001hku.1	-	c.5354C>G	c.(5353-5355)ACA>AGA	p.T1785R		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1785	Laminin G-like 2.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.104218	127.225724	252.798754	84	722	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216251649	216251649	17598	1	G	C	C	C	624	48	USH2A	3	3
USH2A	7399	broad.mit.edu	37	1	216372980	216372980	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216372980G>A	uc001hku.1	-	c.3800C>T	c.(3799-3801)GCG>GTG	p.A1267V	USH2A_uc001hkv.2_Missense_Mutation_p.A1267V	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1267	Fibronectin type-III 3.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.139665	31.250438	53.71198	25	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216372980	216372980	17598	1	G	A	A	A	494	38	USH2A	1	1
LYPLAL1	127018	broad.mit.edu	37	1	219383918	219383918	+	Nonsense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:219383918A>T	uc001hlq.3	+	c.406A>T	c.(406-408)AGA>TGA	p.R136*	LYPLAL1_uc001hlr.3_Nonsense_Mutation_p.R120*|LYPLAL1_uc001hls.3_Nonsense_Mutation_p.R12*|LYPLAL1_uc001hlt.3_Nonsense_Mutation_p.R12*|LYPLAL1_uc009xds.2_Nonsense_Mutation_p.R85*	NM_138794	NP_620149	Q5VWZ2	LYPL1_HUMAN	lysophospholipase-like 1	136						cytoplasm	lysophospholipase activity				0				GBM - Glioblastoma multiforme(131;0.055)|all cancers(67;0.105)|OV - Ovarian serous cystadenocarcinoma(81;0.116)										0.117647	11.426037	26.088793	12	90	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	219383918	219383918	9495	1	A	T	T	T	192	15	LYPLAL1	5	3
IARS2	55699	broad.mit.edu	37	1	220311269	220311269	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220311269A>G	uc001hmc.2	+	c.2059A>G	c.(2059-2061)AAA>GAA	p.K687E	IARS2_uc001hmd.2_Missense_Mutation_p.K23E	NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase	687					isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)	2				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)									0.090361	3.299456	31.431077	15	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220311269	220311269	7774	1	A	G	G	G	65	5	IARS2	4	4
MARK1	4139	broad.mit.edu	37	1	220825386	220825386	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220825386G>T	uc009xdw.2	+	c.1630G>T	c.(1630-1632)GTC>TTC	p.V544F	MARK1_uc001hmn.3_Missense_Mutation_p.V544F|MARK1_uc010pun.1_Missense_Mutation_p.V544F|MARK1_uc001hmm.3_Missense_Mutation_p.V522F	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	544				V -> A (in Ref. 4; BAB55152).	intracellular protein kinase cascade|protein phosphorylation	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|central_nervous_system(2)|stomach(1)|lung(1)	7				GBM - Glioblastoma multiforme(131;0.0407)						258				0.103659	15.365556	41.000466	17	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220825386	220825386	9695	1	G	T	T	T	624	48	MARK1	2	2
OBSCN	84033	broad.mit.edu	37	1	228511036	228511036	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228511036G>T	uc009xez.1	+	c.15381G>T	c.(15379-15381)GTG>GTT	p.V5127V	OBSCN_uc001hsn.2_Silent_p.V5127V	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	5127	Ig-like 49.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.157895	10.323242	14.566424	6	32	KEEP	---	---	---	---	capture		Silent	SNP	228511036	228511036	11217	1	G	T	T	T	613	48	OBSCN	2	2
PCNXL2	80003	broad.mit.edu	37	1	233394394	233394394	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:233394394C>A	uc001hvl.2	-	c.1214G>T	c.(1213-1215)AGT>ATT	p.S405I	PCNXL2_uc009xfu.2_Non-coding_Transcript|PCNXL2_uc009xfv.1_Non-coding_Transcript	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	405						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)												0.111111	29.509284	67.198893	28	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	233394394	233394394	12012	1	C	A	A	A	260	20	PCNXL2	2	2
ERO1LB	56605	broad.mit.edu	37	1	236384244	236384244	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236384244G>A	uc001hxt.2	-	c.1231C>T	c.(1231-1233)CTG>TTG	p.L411L		NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta	411					electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)											0.091954	5.536915	20.119813	8	79	KEEP	---	---	---	---	capture		Silent	SNP	236384244	236384244	5433	1	G	A	A	A	451	35	ERO1LB	2	2
CHRM3	1131	broad.mit.edu	37	1	240072343	240072344	+	Missense_Mutation	DNP	GG	CT	CT			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:240072343_240072344GG>CT	uc001hyp.2	+	c.1592_1593GG>CT	c.(1591-1593)TGG>TCT	p.W531S		NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	531	Helical; Name=7; (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)									0.261364	145.468813	154.538705	46	130	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	240072343	240072344	3512	1	GG	CT	CT	CT	611	47	CHRM3	3	3
FMN2	56776	broad.mit.edu	37	1	240370500	240370500	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:240370500C>A	uc010pye.1	+	c.2400C>A	c.(2398-2400)GTC>GTA	p.V800V	FMN2_uc010pyd.1_Silent_p.V796V	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	796	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|large_intestine(1)|central_nervous_system(1)	9	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)							1289				0.27381	99.143845	106.915198	46	122	KEEP	---	---	---	---	capture		Silent	SNP	240370500	240370500	6192	1	C	A	A	A	379	30	FMN2	2	2
MYOM3	127294	broad.mit.edu	37	1	24433662	24433662	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:24433662C>T	uc001bin.3	-	c.303G>A	c.(301-303)CGG>CGA	p.R101R	MYOM3_uc001bio.2_Silent_p.R101R|MYOM3_uc001bip.1_5'UTR	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3	101										ovary(1)	1		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)										0.15	5.610768	7.960308	3	17	KEEP	---	---	---	---	capture		Silent	SNP	24433662	24433662	10488	1	C	T	T	T	275	22	MYOM3	2	2
OR6F1	343169	broad.mit.edu	37	1	247875336	247875336	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247875336C>A	uc001idj.1	-	c.722G>T	c.(721-723)TGC>TTC	p.C241F		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)											0.170543	83.137853	109.629198	44	214	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247875336	247875336	11611	1	C	A	A	A	325	25	OR6F1	2	2
OR2L3	391192	broad.mit.edu	37	1	248224602	248224602	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248224602G>T	uc001idx.1	+	c.619G>T	c.(619-621)GTG>TTG	p.V207L	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	207	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)											0.063123	-14.41867	45.395236	19	282	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248224602	248224602	11414	1	G	T	T	T	520	40	OR2L3	1	1
OR2M5	127059	broad.mit.edu	37	1	248308701	248308701	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248308701C>A	uc010pze.1	+	c.252C>A	c.(250-252)AAC>AAA	p.N84K		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	84	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)											0.271364	466.939928	498.41066	181	486	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248308701	248308701	11419	1	C	A	A	A	259	20	OR2M5	2	2
OR2T6	254879	broad.mit.edu	37	1	248551725	248551725	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248551725G>T	uc001iei.1	+	c.816G>T	c.(814-816)AAG>AAT	p.K272N		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	272	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.091549	0.859606	24.754903	13	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248551725	248551725	11435	1	G	T	T	T	451	35	OR2T6	2	2
OR2T34	127068	broad.mit.edu	37	1	248737350	248737350	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248737350C>G	uc001iep.1	-	c.709G>C	c.(709-711)GCC>CCC	p.A237P		NM_001001821	NP_001001821	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T,	237	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.091873	20.622427	68.350899	26	257	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248737350	248737350	11431	1	C	G	G	G	351	27	OR2T34	3	3
SH3BP5L	80851	broad.mit.edu	37	1	249107242	249107242	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:249107242G>A	uc001iew.1	-	c.657C>T	c.(655-657)ATC>ATT	p.I219I	SH3BP5L_uc010pzp.1_Silent_p.I112I|SH3BP5L_uc010pzq.1_Silent_p.I187I|SH3BP5L_uc001iev.1_Silent_p.I100I	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	219	Potential.										0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)											0.089431	0.736354	21.673053	11	112	KEEP	---	---	---	---	capture		Silent	SNP	249107242	249107242	14739	1	G	A	A	A	473	37	SH3BP5L	1	1
MATN1	4146	broad.mit.edu	37	1	31194492	31194492	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:31194492G>T	uc001brz.2	-	c.201C>A	c.(199-201)GTC>GTA	p.V67V	MATN1_uc001bsa.1_5'Flank	NM_002379	NP_002370	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein precursor	67	VWFA 1.				protein complex assembly	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			central_nervous_system(1)	1		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)										0.169903	55.985984	77.245239	35	171	KEEP	---	---	---	---	capture		Silent	SNP	31194492	31194492	9717	1	G	T	T	T	574	45	MATN1	2	2
COL16A1	1307	broad.mit.edu	37	1	32163594	32163594	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:32163594G>T	uc001btk.1	-	c.570C>A	c.(568-570)TCC>TCA	p.S190S	COL16A1_uc001btj.1_Silent_p.S19S|COL16A1_uc001btl.3_Silent_p.S190S	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	190	TSP N-terminal.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		Colon(143;498 1786 21362 25193 36625)								0.081081	-3.410345	9.839991	6	68	KEEP	---	---	---	---	capture		Silent	SNP	32163594	32163594	3811	1	G	T	T	T	444	35	COL16A1	2	2
BEST4	266675	broad.mit.edu	37	1	45253101	45253101	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:45253101G>A	uc001cmm.2	-	c.190C>T	c.(190-192)CAG>TAG	p.Q64*		NM_153274	NP_695006	Q8NFU0	BEST4_HUMAN	bestrophin 4	64	Extracellular (Potential).					chloride channel complex|plasma membrane	chloride channel activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.129808	56.880231	112.424147	54	362	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	45253101	45253101	1430	1	G	A	A	A	585	45	BEST4	5	2
DMRTA2	63950	broad.mit.edu	37	1	50885024	50885024	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:50885024C>T	uc010ona.1	-	c.942G>A	c.(940-942)CGG>CGA	p.R314R	DMRTA2_uc010onb.1_Silent_p.R314R	NM_032110	NP_115486	Q96SC8	DMTA2_HUMAN	DMRT-like family A2	314	Gly-rich.				regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0						Colon(196;1651 2045 3292 36497 38236)|Esophageal Squamous(2;257 258 11567 27043 43804)								0.195652	16.043986	20.02209	9	37	KEEP	---	---	---	---	capture		Silent	SNP	50885024	50885024	4769	1	C	T	T	T	379	30	DMRTA2	2	2
YIPF1	54432	broad.mit.edu	37	1	54348884	54348884	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:54348884G>C	uc001cvu.2	-	c.97C>G	c.(97-99)CCT>GCT	p.P33A	YIPF1_uc001cvv.2_Non-coding_Transcript|YIPF1_uc001cvw.2_Non-coding_Transcript|YIPF1_uc001cvx.2_Non-coding_Transcript|YIPF1_uc001cvy.2_Non-coding_Transcript	NM_018982	NP_061855	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	33	Cytoplasmic (Potential).					integral to membrane|transport vesicle				large_intestine(1)|ovary(1)	2														0.054645	-9.908709	28.327085	10	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54348884	54348884	18060	1	G	C	C	C	533	41	YIPF1	3	3
C1orf173	127254	broad.mit.edu	37	1	75055428	75055428	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75055428G>T	uc001dgg.2	-	c.2063C>A	c.(2062-2064)TCC>TAC	p.S688Y	C1orf173_uc001dgi.3_Missense_Mutation_p.S482Y	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	688	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.145631	59.551789	96.906993	45	264	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75055428	75055428	2081	1	G	T	T	T	533	41	C1orf173	2	2
C1orf173	127254	broad.mit.edu	37	1	75055641	75055641	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75055641C>G	uc001dgg.2	-	c.1850G>C	c.(1849-1851)AGG>ACG	p.R617T	C1orf173_uc001dgi.3_Missense_Mutation_p.R411T	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	617	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.123188	24.970794	44.148012	17	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75055641	75055641	2081	1	C	G	G	G	312	24	C1orf173	3	3
SYDE2	84144	broad.mit.edu	37	1	85648858	85648858	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:85648858A>G	uc009wcm.2	-	c.1467T>C	c.(1465-1467)AAT>AAC	p.N489N	SYDE2_uc001dku.3_Silent_p.N489N	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	489					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)										0.098485	16.188263	37.462476	13	119	KEEP	---	---	---	---	capture		Silent	SNP	85648858	85648858	15957	1	A	G	G	G	206	16	SYDE2	4	4
COL24A1	255631	broad.mit.edu	37	1	86488678	86488678	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86488678G>A	uc001dlj.2	-	c.2062C>T	c.(2062-2064)CCT>TCT	p.P688S	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_Non-coding_Transcript|COL24A1_uc010ose.1_Non-coding_Transcript|COL24A1_uc010osf.1_Non-coding_Transcript	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	688	Collagen-like 3.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)	4				all cancers(265;0.0627)|Epithelial(280;0.0689)										0.113208	6.810359	14.636374	6	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86488678	86488678	3821	1	G	A	A	A	559	43	COL24A1	2	2
LRRC8C	84230	broad.mit.edu	37	1	90179864	90179864	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:90179864C>T	uc001dnl.3	+	c.1735C>T	c.(1735-1737)CTG>TTG	p.L579L		NM_032270	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member	579	LRR 8.					endoplasmic reticulum membrane|integral to membrane				ovary(3)|central_nervous_system(1)|pancreas(1)	5		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)										0.094828	7.530914	26.656821	11	105	KEEP	---	---	---	---	capture		Silent	SNP	90179864	90179864	9399	1	C	T	T	T	363	28	LRRC8C	2	2
GFI1	2672	broad.mit.edu	37	1	92948493	92948493	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:92948493C>T	uc001dou.3	-	c.226G>A	c.(226-228)GAA>AAA	p.E76K	GFI1_uc001dov.3_Missense_Mutation_p.E76K|GFI1_uc001dow.3_Missense_Mutation_p.E76K	NM_001127215	NP_001120687	Q99684	GFI1_HUMAN	growth factor independent 1	76				DSCEG -> RQLRS (in Ref. 1; AAB37272).	negative regulation of calcidiol 1-monooxygenase activity|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of vitamin D biosynthetic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|transcription, DNA-dependent|viral reproduction	nucleus	promoter binding|protein binding|zinc ion binding			large_intestine(1)	1		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)										0.182796	31.221534	40.00984	17	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92948493	92948493	6607	1	C	T	T	T	403	31	GFI1	1	1
MACROD2	140733	broad.mit.edu	37	20	14066278	14066278	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:14066278C>T	uc002wou.2	+	c.175C>T	c.(175-177)CAG>TAG	p.Q59*	MACROD2_uc002wot.2_Nonsense_Mutation_p.Q59*	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1	59	Macro.										0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)												0.210526	17.378629	20.324938	8	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	14066278	14066278	9523	20	C	T	T	T	377	29	MACROD2	5	2
C20orf3	57136	broad.mit.edu	37	20	24964571	24964571	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:24964571C>A	uc002wtz.2	-	c.180G>T	c.(178-180)CTG>CTT	p.L60L	C20orf3_uc002wty.2_Silent_p.L60L|C20orf3_uc010zsw.1_Silent_p.L60L	NM_020531	NP_065392	Q9HDC9	APMAP_HUMAN	chromosome 20 open reading frame 3	60	Helical; Signal-anchor for type II membrane protein; (Potential).				biosynthetic process	cell surface|integral to membrane	arylesterase activity|strictosidine synthase activity			ovary(1)	1														0.179348	61.548844	79.384901	33	151	KEEP	---	---	---	---	capture		Silent	SNP	24964571	24964571	2189	20	C	A	A	A	314	25	C20orf3	2	2
TPX2	22974	broad.mit.edu	37	20	30388777	30388777	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30388777A>G	uc010gdv.1	+	c.2246A>G	c.(2245-2247)CAT>CGT	p.H749R	TPX2_uc002wwp.1_Missense_Mutation_p.H713R	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog	713					activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)											0.318182	389.576066	402.488365	140	300	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30388777	30388777	16976	20	A	G	G	G	104	8	TPX2	4	4
BPIL3	128859	broad.mit.edu	37	20	31619551	31619551	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31619551G>T	uc010zuc.1	+	c.97_splice	c.e1+1	p.Q33_splice	BPIL3_uc010zud.1_5'UTR	NM_174897	NP_777557			bactericidal/permeability-increasing							extracellular region	lipid binding			ovary(1)|pancreas(1)	2														0.15942	21.382781	29.005088	11	58	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	31619551	31619551	1521	20	G	T	T	T	520	40	BPIL3	5	1
GDF5	8200	broad.mit.edu	37	20	34021748	34021748	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34021748G>T	uc010gfc.1	-	c.1465C>A	c.(1465-1467)CAG>AAG	p.Q489K	GDF5_uc002xck.1_Missense_Mutation_p.Q489K|GDF5_uc010zvc.1_Missense_Mutation_p.Q489K	NM_000557	NP_000548	P43026	GDF5_HUMAN	growth differentiation factor 5 preproprotein	489					cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)											0.135338	22.749637	39.908787	18	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34021748	34021748	6584	20	G	T	T	T	598	46	GDF5	2	2
MYT1	4661	broad.mit.edu	37	20	62839147	62839147	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62839147G>T	uc002yii.2	+	c.598G>T	c.(598-600)GAG>TAG	p.E200*	MYT1_uc002yih.2_Intron|MYT1_uc002yij.2_5'UTR	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	200	Glu-rich.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GBM(59;481 1041 20555 21139 33705)				1819				0.121212	9.621854	23.562684	12	87	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	62839147	62839147	10501	20	G	T	T	T	533	41	MYT1	5	2
ANGPT4	51378	broad.mit.edu	37	20	869027	869027	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:869027G>A	uc002wei.2	-	c.521C>T	c.(520-522)ACC>ATC	p.T174I	ANGPT4_uc010zpn.1_Missense_Mutation_p.T168I	NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4 precursor	174	Potential.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						Pancreas(181;481 2077 3259 31286 49856)								0.177966	37.514127	49.031308	21	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	869027	869027	615	20	G	A	A	A	572	44	ANGPT4	2	2
TPTE	7179	broad.mit.edu	37	21	10920118	10920118	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:10920118C>G	uc002yip.1	-	c.1136G>C	c.(1135-1137)AGC>ACC	p.S379T	TPTE_uc002yis.1_Non-coding_Transcript|TPTE_uc002yiq.1_Missense_Mutation_p.S361T|TPTE_uc002yir.1_Missense_Mutation_p.S341T|TPTE_uc010gkv.1_Missense_Mutation_p.S241T	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	379	Phosphatase tensin-type.				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)										0.042553	-20.301096	11.652655	6	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10920118	10920118	16974	21	C	G	G	G	364	28	TPTE	3	3
CYYR1	116159	broad.mit.edu	37	21	27945230	27945230	+	Silent	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:27945230T>A	uc002yme.2	-	c.30A>T	c.(28-30)CCA>CCT	p.P10P	CYYR1_uc002ymd.2_Silent_p.P10P|CYYR1_uc011ack.1_Non-coding_Transcript	NM_052954	NP_443186	Q96J86	CYYR1_HUMAN	cysteine and tyrosine-rich 1 protein precursor	10						integral to membrane					0														0.147826	26.313323	39.999163	17	98	KEEP	---	---	---	---	capture		Silent	SNP	27945230	27945230	4376	21	T	A	A	A	704	55	CYYR1	3	3
N6AMT1	29104	broad.mit.edu	37	21	30252230	30252230	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:30252230C>A	uc002ymo.1	-	c.358G>T	c.(358-360)GTG>TTG	p.V120L	N6AMT1_uc002ymp.1_Intron|N6AMT1_uc002ymq.1_Non-coding_Transcript	NM_013240	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1	120					positive regulation of cell growth	protein complex	nucleic acid binding|protein binding|protein methyltransferase activity				0														0.136842	43.415648	67.675007	26	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30252230	30252230	10509	21	C	A	A	A	234	18	N6AMT1	2	2
KRTAP8-1	337879	broad.mit.edu	37	21	32185390	32185390	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32185390C>A	uc002you.2	-	c.149G>T	c.(148-150)GGG>GTG	p.G50V		NM_175857	NP_787053	Q8IUC2	KRA81_HUMAN	keratin associated protein 8-1	50	12 X 2 AA repeats of G-[YCGS].					intermediate filament					0														0.126126	11.857459	27.035254	14	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32185390	32185390	8895	21	C	A	A	A	286	22	KRTAP8-1	2	2
ABCG1	9619	broad.mit.edu	37	21	43706025	43706025	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43706025G>T	uc011aev.1	+	c.927G>T	c.(925-927)CGG>CGT	p.R309R	ABCG1_uc002zan.2_Silent_p.R300R|ABCG1_uc002zam.2_Silent_p.R276R|ABCG1_uc002zao.2_Silent_p.R295R|ABCG1_uc002zap.2_Silent_p.R298R|ABCG1_uc002zaq.2_Silent_p.R298R|ABCG1_uc002zar.2_Silent_p.R309R|ABCG1_uc010gpb.1_5'UTR	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1	298	Cytoplasmic (Potential).|ABC transporter.				amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|integral to plasma membrane|recycling endosome	ADP binding|ATP binding|cholesterol binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid binding|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)	2					Adenosine triphosphate(DB00171)									0.130435	55.728237	104.651824	48	320	KEEP	---	---	---	---	capture		Silent	SNP	43706025	43706025	69	21	G	T	T	T	548	43	ABCG1	2	2
TMPRSS3	64699	broad.mit.edu	37	21	43796717	43796717	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43796717T>C	uc002zbb.2	-	c.1127A>G	c.(1126-1128)TAC>TGC	p.Y376C	TMPRSS3_uc002zay.2_Missense_Mutation_p.Y133C|TMPRSS3_uc002zaz.2_Missense_Mutation_p.Y249C|TMPRSS3_uc002zba.2_Missense_Mutation_p.Y249C|TMPRSS3_uc002zbc.2_Missense_Mutation_p.Y375C	NM_024022	NP_076927	P57727	TMPS3_HUMAN	transmembrane protease, serine 3 isoform 1	376	Peptidase S1.|Extracellular (Potential).			ICNHRDVYGGIISPSMLCAGYLTGGVD -> DLQPQGRVRW HHLPLHALRGLPDGWRWN (in Ref. 1; AAG37012).	cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3														0.079848	3.460589	50.997977	21	242	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43796717	43796717	16789	21	T	C	C	C	741	57	TMPRSS3	4	4
PKNOX1	5316	broad.mit.edu	37	21	44441505	44441505	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:44441505G>T	uc002zcq.1	+	c.813G>T	c.(811-813)ACG>ACT	p.T271T	PKNOX1_uc002zcp.1_Silent_p.T271T|PKNOX1_uc011aex.1_Silent_p.T154T	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	271	Homeobox; TALE-type.						sequence-specific DNA binding|specific RNA polymerase II transcription factor activity			large_intestine(2)	2														0.145038	32.438749	48.31807	19	112	KEEP	---	---	---	---	capture		Silent	SNP	44441505	44441505	12407	21	G	T	T	T	470	37	PKNOX1	1	1
TUBA8	51807	broad.mit.edu	37	22	18613793	18613793	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:18613793G>A	uc002znw.1	+	c.1312G>A	c.(1312-1314)GAA>AAA	p.E438K	TUBA8_uc002znr.2_Missense_Mutation_p.E348K|TUBA8_uc002znv.1_Missense_Mutation_p.E414K|TUBA8_uc002znx.1_Intron	NM_018943	NP_061816	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	414					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0														0.178571	40.726873	51.623499	20	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18613793	18613793	17305	22	G	A	A	A	533	41	TUBA8	2	2
HPS4	89781	broad.mit.edu	37	22	26860726	26860726	+	Silent	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26860726T>A	uc003acl.2	-	c.870A>T	c.(868-870)ACA>ACT	p.T290T	HPS4_uc003aci.2_Silent_p.T285T|HPS4_uc003acj.2_Silent_p.T154T|HPS4_uc003ack.2_Silent_p.T81T|HPS4_uc003acn.2_Silent_p.T136T|HPS4_uc010gvd.1_Silent_p.T308T|HPS4_uc003ach.2_Silent_p.T25T	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	290					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0														0.124031	20.628742	38.448641	16	113	KEEP	---	---	---	---	capture		Silent	SNP	26860726	26860726	7633	22	T	A	A	A	652	51	HPS4	3	3
SLC5A1	6523	broad.mit.edu	37	22	32482262	32482262	+	Silent	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32482262T>A	uc003amc.2	+	c.1077T>A	c.(1075-1077)GTT>GTA	p.V359V	SLC5A1_uc011alz.1_Silent_p.V232V	NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose	359	Extracellular (Potential).				carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding				0														0.160377	63.029535	86.297532	34	178	KEEP	---	---	---	---	capture		Silent	SNP	32482262	32482262	15158	22	T	A	A	A	808	63	SLC5A1	3	3
SLC5A4	6527	broad.mit.edu	37	22	32631037	32631037	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32631037G>T	uc003ami.2	-	c.708C>A	c.(706-708)TAC>TAA	p.Y236*		NM_014227	NP_055042	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (low affinity glucose	236	Extracellular (Potential).				carbohydrate transport|sodium ion transport	integral to membrane	symporter activity				0														0.140449	88.84449	133.252395	50	306	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	32631037	32631037	15164	22	G	T	T	T	516	40	SLC5A4	5	1
SYN3	8224	broad.mit.edu	37	22	32934062	32934062	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32934062T>C	uc003amx.2	-	c.952A>G	c.(952-954)ACA>GCA	p.T318A	SYN3_uc003amy.2_Missense_Mutation_p.T318A|SYN3_uc003amz.2_Missense_Mutation_p.T317A	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa	318	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity				0										35				0.085427	7.484571	42.106588	17	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32934062	32934062	15963	22	T	C	C	C	767	59	SYN3	4	4
PLA2G6	8398	broad.mit.edu	37	22	38508177	38508177	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:38508177G>A	uc003auy.1	-	c.2412C>T	c.(2410-2412)CTC>CTT	p.L804L	PLA2G6_uc003auz.1_Silent_p.L750L|PLA2G6_uc003ava.1_Silent_p.L804L|PLA2G6_uc003avb.2_Silent_p.L750L|BAIAP2L2_uc003auw.2_5'Flank|PLA2G6_uc003aux.1_3'UTR	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a	804					cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)									0.214286	7.22165	8.273797	3	11	KEEP	---	---	---	---	capture		Silent	SNP	38508177	38508177	12434	22	G	A	A	A	418	33	PLA2G6	2	2
TBC1D8	11138	broad.mit.edu	37	2	101648757	101648757	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:101648757G>T	uc010fiv.2	-	c.1864C>A	c.(1864-1866)CCC>ACC	p.P622T	TBC1D8_uc002tau.3_Missense_Mutation_p.P379T	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	622	Rab-GAP TBC.				blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3														0.086022	-1.543612	14.591659	8	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101648757	101648757	16151	2	G	T	T	T	546	42	TBC1D8	2	2
IL1F10	84639	broad.mit.edu	37	2	113832364	113832364	+	Silent	SNP	C	T	T	rs34320972		TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:113832364C>T	uc002tiu.2	+	c.183C>T	c.(181-183)ATC>ATT	p.I61I	IL1F10_uc002tiv.2_Silent_p.I61I|IL1F10_uc002tiw.2_Silent_p.I53I	NM_173161	NP_775184	Q8WWZ1	IL1FA_HUMAN	interleukin 1 family, member 10	61						extracellular space	cytokine activity|interleukin-1 receptor antagonist activity			ovary(1)	1														0.053191	-20.256753	19.324566	10	178	KEEP	---	---	---	---	capture		Silent	SNP	113832364	113832364	7953	2	C	T	T	T	382	30	IL1F10	2	2
GLI2	2736	broad.mit.edu	37	2	121726405	121726405	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:121726405C>G	uc010flp.2	+	c.759C>G	c.(757-759)CCC>CCG	p.P253P	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Missense_Mutation_p.Q124E|GLI2_uc010flo.1_Silent_p.P128P|GLI2_uc002tmw.1_Silent_p.P253P	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	253					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(7)|central_nervous_system(1)	8	Renal(3;0.0496)	Prostate(154;0.0623)								376				0.123377	29.409746	50.783993	19	135	KEEP	---	---	---	---	capture		Silent	SNP	121726405	121726405	6706	2	C	G	G	G	262	21	GLI2	3	3
CNTNAP5	129684	broad.mit.edu	37	2	125555733	125555733	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125555733C>A	uc010flu.2	+	c.3053C>A	c.(3052-3054)CCT>CAT	p.P1018H	CNTNAP5_uc002tno.2_Missense_Mutation_p.P1017H	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1017	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.066667	-5.189844	9.416488	5	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125555733	125555733	3788	2	C	A	A	A	312	24	CNTNAP5	2	2
NCKAP5	344148	broad.mit.edu	37	2	133887593	133887593	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:133887593G>T	uc002ttp.2	-	c.298C>A	c.(298-300)CGC>AGC	p.R100S	NCKAP5_uc002ttq.2_Missense_Mutation_p.R100S|NCKAP5_uc002ttt.1_Missense_Mutation_p.R100S|NCKAP5_uc002tts.1_Missense_Mutation_p.R75S	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	100	Potential.						protein binding				0														0.096774	2.702436	7.752099	3	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133887593	133887593	10622	2	G	T	T	T	520	40	NCKAP5	1	1
LRP1B	53353	broad.mit.edu	37	2	141130585	141130585	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141130585C>A	uc002tvj.1	-	c.10760G>T	c.(10759-10761)TGT>TTT	p.C3587F		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3587	Extracellular (Potential).|LDL-receptor class A 27.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.096234	15.915493	55.075947	23	216	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141130585	141130585	9328	2	C	A	A	A	221	17	LRP1B	2	2
BAZ2B	29994	broad.mit.edu	37	2	160239224	160239224	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:160239224G>A	uc002uao.2	-	c.3851C>T	c.(3850-3852)CCC>CTC	p.P1284L	BAZ2B_uc002uap.2_Missense_Mutation_p.P1248L	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1284					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|transcription regulator activity|zinc ion binding			ovary(3)	3														0.12987	14.923316	25.166118	10	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160239224	160239224	1353	2	G	A	A	A	559	43	BAZ2B	2	2
XIRP2	129446	broad.mit.edu	37	2	168102029	168102029	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168102029A>T	uc002udx.2	+	c.4127A>T	c.(4126-4128)CAA>CTA	p.Q1376L	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.Q1201L|XIRP2_uc010fpq.2_Missense_Mutation_p.Q1154L|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1201					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.150794	33.951945	48.666666	19	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168102029	168102029	18011	2	A	T	T	T	65	5	XIRP2	3	3
XIRP2	129446	broad.mit.edu	37	2	168106863	168106863	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168106863G>A	uc002udx.2	+	c.8961G>A	c.(8959-8961)CTG>CTA	p.L2987L	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.L2812L|XIRP2_uc010fpq.2_Silent_p.L2765L|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Silent_p.L333L	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2812					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.107692	13.316228	43.109329	21	174	KEEP	---	---	---	---	capture		Silent	SNP	168106863	168106863	18011	2	G	A	A	A	574	45	XIRP2	2	2
HOXD12	3238	broad.mit.edu	37	2	176965302	176965302	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:176965302C>A	uc010zev.1	+	c.627C>A	c.(625-627)TAC>TAA	p.Y209*	HOXD12_uc010zew.1_Missense_Mutation_p.H219N	NM_021193	NP_067016	P35452	HXD12_HUMAN	homeobox D12	209	Homeobox.				regulation of transcription, DNA-dependent	nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)										0.222222	14.940755	16.85352	6	21	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	176965302	176965302	7613	2	C	A	A	A	220	17	HOXD12	5	2
TTN	7273	broad.mit.edu	37	2	179584084	179584084	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179584084T>C	uc010zfg.1	-	c.20301A>G	c.(20299-20301)TCA>TCG	p.S6767S	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.S3428S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3083										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.098485	14.059396	56.653524	26	238	KEEP	---	---	---	---	capture		Silent	SNP	179584084	179584084	17290	2	T	C	C	C	704	55	TTN	4	4
FRZB	2487	broad.mit.edu	37	2	183723563	183723563	+	Splice_Site_SNP	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:183723563T>A	uc002upa.1	-	c.479_splice	c.e2-1	p.D160_splice		NM_001463	NP_001454			frizzled-related protein precursor						brain development|cochlea morphogenesis|gonad development|mammary gland involution|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of hepatocyte differentiation|positive regulation of apoptosis|positive regulation of fat cell differentiation|regulation of gene-specific transcription from RNA polymerase II promoter|skeletal system development|vasculature development|Wnt receptor signaling pathway	cytoplasm|extracellular space|membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)											0.228758	90.852893	101.171275	35	118	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	183723563	183723563	6315	2	T	A	A	A	715	55	FRZB	5	3
PARD3B	117583	broad.mit.edu	37	2	205978257	205978257	+	Silent	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:205978257A>T	uc002var.1	+	c.636A>T	c.(634-636)CCA>CCT	p.P212P	PARD3B_uc010fub.1_Silent_p.P212P|PARD3B_uc002vao.1_Silent_p.P212P|PARD3B_uc002vap.1_Silent_p.P212P|PARD3B_uc002vaq.1_Silent_p.P212P	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	212	PDZ 1.				cell cycle|cell division	endomembrane system|tight junction				ovary(1)|breast(1)	2		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)										0.179775	36.655037	45.231138	16	73	KEEP	---	---	---	---	capture		Silent	SNP	205978257	205978257	11861	2	A	T	T	T	93	8	PARD3B	3	3
ACCN4	55515	broad.mit.edu	37	2	220397143	220397143	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220397143G>T	uc002vlz.2	+	c.1343G>T	c.(1342-1344)CGC>CTC	p.R448L	ACCN4_uc010fwi.1_Missense_Mutation_p.R448L|ACCN4_uc010fwj.1_Missense_Mutation_p.R448L|ACCN4_uc002vly.1_3'UTR|ACCN4_uc002vma.2_Missense_Mutation_p.R448L|ACCN4_uc002vmb.2_Missense_Mutation_p.R102L	NM_018674	NP_061144	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 1	448	Extracellular (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)										0.152778	18.193236	26.488416	11	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220397143	220397143	132	2	G	T	T	T	494	38	ACCN4	1	1
EPHA4	2043	broad.mit.edu	37	2	222428583	222428583	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:222428583C>A	uc002vmq.2	-	c.691G>T	c.(691-693)GGC>TGC	p.G231C	EPHA4_uc002vmr.2_Missense_Mutation_p.G231C|EPHA4_uc010zlm.1_Missense_Mutation_p.G172C|EPHA4_uc010zln.1_Missense_Mutation_p.G231C	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor	231	Cys-rich.|Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			lung(3)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	9		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)						395				0.140078	44.827671	76.987297	36	221	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	222428583	222428583	5362	2	C	A	A	A	312	24	EPHA4	2	2
FAM124B	79843	broad.mit.edu	37	2	225266018	225266018	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:225266018G>T	uc002vnx.2	-	c.468C>A	c.(466-468)TAC>TAA	p.Y156*	FAM124B_uc002vnw.2_Nonsense_Mutation_p.Y156*	NM_001122779	NP_001116251	Q9H5Z6	F124B_HUMAN	hypothetical protein LOC79843 isoform a	156							protein binding			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)										0.108108	17.902375	40.426652	16	132	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	225266018	225266018	5623	2	G	T	T	T	516	40	FAM124B	5	1
KIAA1486	57624	broad.mit.edu	37	2	226447291	226447291	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:226447291C>T	uc002voe.2	+	c.1158C>T	c.(1156-1158)CAC>CAT	p.H386H	KIAA1486_uc010fxa.1_Intron|KIAA1486_uc002vof.1_Silent_p.H156H	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	386	Pro-rich.									ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)										0.214286	5.818065	6.873353	3	11	KEEP	---	---	---	---	capture		Silent	SNP	226447291	226447291	8546	2	C	T	T	T	246	19	KIAA1486	1	1
PID1	55022	broad.mit.edu	37	2	230020666	230020666	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:230020666C>A	uc002vpr.3	-	c.144G>T	c.(142-144)ATG>ATT	p.M48I	PID1_uc002vps.3_Missense_Mutation_p.M46I|PID1_uc002vpt.3_Missense_Mutation_p.M15I|PID1_uc002vpu.3_Intron	NM_001100818	NP_001094288	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	48						cytoplasm				breast(3)	3		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)										0.134021	36.206159	61.423114	26	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	230020666	230020666	12306	2	C	A	A	A	325	25	PID1	2	2
COL6A3	1293	broad.mit.edu	37	2	238289824	238289824	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:238289824C>A	uc002vwl.2	-	c.1631G>T	c.(1630-1632)CGG>CTG	p.R544L	COL6A3_uc002vwo.2_Missense_Mutation_p.R338L|COL6A3_uc010znj.1_Missense_Mutation_p.R137L|COL6A3_uc002vwq.2_Missense_Mutation_p.R338L|COL6A3_uc002vwr.2_Missense_Mutation_p.R137L|COL6A3_uc010znk.1_Missense_Mutation_p.R544L	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	544	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.144737	42.015483	69.741155	33	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	238289824	238289824	3839	2	C	A	A	A	299	23	COL6A3	1	1
PPP1R7	5510	broad.mit.edu	37	2	242092932	242092932	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242092932G>T	uc002wat.1	+	c.94G>T	c.(94-96)GGG>TGG	p.G32W	PPP1R7_uc010fzm.1_Missense_Mutation_p.G16W|PPP1R7_uc002war.2_Missense_Mutation_p.G32W|PPP1R7_uc002was.2_Missense_Mutation_p.G32W|PPP1R7_uc002wau.1_Intron|PPP1R7_uc002wav.1_De_novo_Start_OutOfFrame	NM_002712	NP_002703	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	32						cytoplasm|nucleus	protein binding|protein phosphatase type 1 regulator activity			ovary(2)	2		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		NSCLC(62;446 1299 5417 11238 27640)								0.17094	31.627068	43.614813	20	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242092932	242092932	12812	2	G	T	T	T	455	35	PPP1R7	2	2
SLC8A1	6546	broad.mit.edu	37	2	40657385	40657385	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:40657385G>T	uc002rrx.2	-	c.36C>A	c.(34-36)ACC>ACA	p.T12T	SLC8A1_uc002rry.2_Silent_p.T12T|SLC8A1_uc002rrz.2_Silent_p.T12T|SLC8A1_uc002rsa.2_Silent_p.T12T|SLC8A1_uc002rsd.3_Silent_p.T12T|SLC8A1_uc002rsb.1_Silent_p.T12T|SLC8A1_uc010fan.1_Silent_p.T12T|SLC8A1_uc002rsc.1_Silent_p.T12T	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	12					cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)									0.196262	37.641963	46.825647	21	86	KEEP	---	---	---	---	capture		Silent	SNP	40657385	40657385	15203	2	G	T	T	T	444	35	SLC8A1	2	2
THADA	63892	broad.mit.edu	37	2	43801863	43801863	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:43801863C>T	uc002rsw.3	-	c.1341G>A	c.(1339-1341)TTG>TTA	p.L447L	THADA_uc002rsx.3_Silent_p.L447L|THADA_uc002rsy.3_Non-coding_Transcript|THADA_uc010fas.1_Non-coding_Transcript|THADA_uc002rsz.2_Silent_p.L157L|THADA_uc002rta.2_Silent_p.L157L|THADA_uc002rtb.1_Silent_p.L447L|THADA_uc002rtc.3_Silent_p.L447L|THADA_uc002rtd.2_Silent_p.L447L	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	447							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)												0.157534	41.922991	58.262654	23	123	KEEP	---	---	---	---	capture		Silent	SNP	43801863	43801863	16368	2	C	T	T	T	272	21	THADA	2	2
PLEKHH2	130271	broad.mit.edu	37	2	43992633	43992633	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:43992633C>T	uc010yny.1	+	c.4378C>T	c.(4378-4380)CCA>TCA	p.P1460S		NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H	1460						cytoplasm|cytoskeleton|integral to membrane	binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)												0.184	44.055418	55.766364	23	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43992633	43992633	12503	2	C	T	T	T	390	30	PLEKHH2	2	2
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48896946	48896946	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48896946C>T	uc002rwp.1	+	c.3176C>T	c.(3175-3177)ACA>ATA	p.T1059I	STON1-GTF2A1L_uc010yol.1_Missense_Mutation_p.T1012I|GTF2A1L_uc002rws.1_Missense_Mutation_p.T355I|GTF2A1L_uc010yom.1_Missense_Mutation_p.T321I|GTF2A1L_uc002rwt.2_Missense_Mutation_p.T355I	NM_172311	NP_758515	B7ZL16	B7ZL16_HUMAN	STON1-GTF2A1L protein	1012					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex	RNA polymerase II transcription factor activity			ovary(3)|pancreas(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)											0.121951	19.473279	42.447686	20	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48896946	48896946	15837	2	C	T	T	T	221	17	STON1-GTF2A1L	2	2
NRXN1	9378	broad.mit.edu	37	2	50765774	50765775	+	Splice_Site_DNP	DNP	CC	AA	AA			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:50765774_50765775CC>AA	uc010fbq.2	-	c.1880_splice	c.e10-1	p.G627_splice	NRXN1_uc002rxb.3_Splice_Site_DNP_p.G259_splice|NRXN1_uc002rxe.3_Splice_Site_DNP_p.G587_splice|NRXN1_uc002rxc.1_Splice_Site_DNP	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.120879	12.957593	25.783885	11	80	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	50765774	50765775	11070	2	CC	AA	AA	AA	234	18	NRXN1	5	2
SERTAD2	9792	broad.mit.edu	37	2	64863748	64863748	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:64863748G>A	uc002sde.1	-	c.258C>T	c.(256-258)TTC>TTT	p.F86F		NM_014755	NP_055570	Q14140	SRTD2_HUMAN	SERTA domain containing 2	86					negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0														0.119048	7.036507	18.976162	10	74	KEEP	---	---	---	---	capture		Silent	SNP	64863748	64863748	14609	2	G	A	A	A	581	45	SERTAD2	2	2
ARHGAP25	9938	broad.mit.edu	37	2	69034445	69034445	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:69034445A>G	uc010fdg.2	+	c.507A>G	c.(505-507)GAA>GAG	p.E169E	ARHGAP25_uc010yqk.1_Silent_p.E143E|ARHGAP25_uc002seu.2_Silent_p.E168E|ARHGAP25_uc010yql.1_Silent_p.E129E|ARHGAP25_uc002sev.2_Silent_p.E162E|ARHGAP25_uc002sew.2_Silent_p.E161E|ARHGAP25_uc002sex.2_Silent_p.E162E|ARHGAP25_uc010fdh.1_Non-coding_Transcript|ARHGAP25_uc002sey.2_5'UTR	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	168	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4														0.218391	55.183204	61.536993	19	68	KEEP	---	---	---	---	capture		Silent	SNP	69034445	69034445	886	2	A	G	G	G	24	2	ARHGAP25	4	4
GFPT1	2673	broad.mit.edu	37	2	69556903	69556903	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:69556903C>A	uc002sfh.2	-	c.1456G>T	c.(1456-1458)GTG>TTG	p.V486L		NM_002056	NP_002047	Q06210	GFPT1_HUMAN	glucosamine-fructose-6-phosphate	504	SIS 1.				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding				0														0.136986	30.395774	49.021454	20	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69556903	69556903	6613	2	C	A	A	A	221	17	GFPT1	2	2
IMMT	10989	broad.mit.edu	37	2	86371798	86371798	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:86371798C>T	uc002sqz.3	-	c.1870G>A	c.(1870-1872)GGG>AGG	p.G624R	IMMT_uc002sqy.3_Missense_Mutation_p.G365R|IMMT_uc002srb.3_Missense_Mutation_p.G613R|IMMT_uc002sra.3_Missense_Mutation_p.G623R|IMMT_uc010ytd.1_Missense_Mutation_p.G612R|IMMT_uc010yte.1_Missense_Mutation_p.G577R	NM_006839	NP_006830	Q16891	IMMT_HUMAN	inner membrane protein, mitochondrial isoform 1	624	Mitochondrial intermembrane (Potential).					integral to mitochondrial inner membrane	protein binding			skin(1)	1														0.123457	35.272876	68.987927	30	213	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86371798	86371798	8019	2	C	T	T	T	273	21	IMMT	2	2
MGAT4A	11320	broad.mit.edu	37	2	99261914	99261914	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99261914T>C	uc002sze.2	-	c.866A>G	c.(865-867)GAG>GGG	p.E289G	C2orf64_uc002sza.2_Non-coding_Transcript|MGAT4A_uc010yvm.1_Missense_Mutation_p.E161G|MGAT4A_uc010fil.2_Missense_Mutation_p.E43G	NM_012214	NP_036346	Q9UM21	MGT4A_HUMAN	alpha-1,3-mannosyl-glycoprotein	289	Lumenal (Potential).				N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding				0														0.059211	-6.642729	24.258882	9	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99261914	99261914	9935	2	T	C	C	C	702	54	MGAT4A	4	4
CD200R1	131450	broad.mit.edu	37	3	112648181	112648181	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112648181C>A	uc003dzj.1	-	c.376G>T	c.(376-378)GAG>TAG	p.E126*	CD200R1_uc003dzk.1_Nonsense_Mutation_p.E103*|CD200R1_uc011bhx.1_Nonsense_Mutation_p.E81*|CD200R1_uc003dzl.1_Nonsense_Mutation_p.E126*|CD200R1_uc003dzm.1_Nonsense_Mutation_p.E103*	NM_138806	NP_620161	Q8TD46	MO2R1_HUMAN	CD200 receptor 1 isoform a	103	Ig-like V-type.|Extracellular (Potential).				interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(2)|pancreas(1)	3														0.219178	99.69772	115.603471	48	171	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	112648181	112648181	3108	3	C	A	A	A	377	29	CD200R1	5	2
FBXO40	51725	broad.mit.edu	37	3	121341414	121341414	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:121341414A>T	uc003eeg.2	+	c.1138A>T	c.(1138-1140)ACT>TCT	p.T380S		NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40	380						centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)										0.248447	96.42999	105.692859	40	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121341414	121341414	5986	3	A	T	T	T	182	14	FBXO40	3	3
ATR	545	broad.mit.edu	37	3	142188251	142188251	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:142188251C>G	uc003eux.3	-	c.6480G>C	c.(6478-6480)TTG>TTC	p.L2160F	ATR_uc003euy.1_Missense_Mutation_p.L46F	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2160	FAT.				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|breast(4)|ovary(3)|skin(2)|stomach(1)|central_nervous_system(1)|liver(1)	17										936				0.078431	5.585698	33.361827	12	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142188251	142188251	1223	3	C	G	G	G	376	29	ATR	3	3
WWTR1	25937	broad.mit.edu	37	3	149374727	149374727	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:149374727C>G	uc003exe.2	-	c.367G>C	c.(367-369)GAG>CAG	p.E123Q	WWTR1_uc003exf.2_Missense_Mutation_p.E123Q|WWTR1_uc011bns.1_Missense_Mutation_p.E123Q|WWTR1_uc003exh.2_Missense_Mutation_p.E123Q	NM_015472	NP_056287	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	123					hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)											0.327273	57.438861	58.890206	18	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149374727	149374727	17991	3	C	G	G	G	403	31	WWTR1	3	3
FAM194A	131831	broad.mit.edu	37	3	150377865	150377865	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:150377865C>G	uc003eyg.2	-	c.1806G>C	c.(1804-1806)AAG>AAC	p.K602N	FAM194A_uc003eyh.2_Missense_Mutation_p.K456N	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	602										ovary(1)|skin(1)	2														0.222222	168.197709	187.336001	60	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150377865	150377865	5737	3	C	G	G	G	415	32	FAM194A	3	3
BCHE	590	broad.mit.edu	37	3	165548428	165548428	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:165548428G>T	uc003fem.3	-	c.394C>A	c.(394-396)CCA>ACA	p.P132T	BCHE_uc003fen.3_Intron	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	132					acetylcholine catabolic process|choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)									0.212291	87.649308	101.348396	38	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165548428	165548428	1379	3	G	T	T	T	572	44	BCHE	2	2
PIK3CA	5290	broad.mit.edu	37	3	178921566	178921566	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:178921566G>A	uc003fjk.2	+	c.1048G>A	c.(1048-1050)GAC>AAC	p.D350N		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	350	C2.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.D350H(1)		breast(1506)|large_intestine(749)|endometrium(244)|urinary_tract(195)|ovary(136)|skin(112)|stomach(89)|thyroid(77)|central_nervous_system(69)|lung(61)|upper_aerodigestive_tract(48)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|kidney(2)|prostate(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3437	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			Colon(199;1504 1750 3362 26421 31210 32040)		57	p.D350N(CAL148-Tumor)	621	TCGA GBM(8;5.49e-07)			0.115607	21.07225	46.249911	20	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178921566	178921566	12337	3	G	A	A	A	429	33	PIK3CA	2	2
MCF2L2	23101	broad.mit.edu	37	3	183013262	183013262	+	Nonsense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183013262T>A	uc003fli.1	-	c.1501A>T	c.(1501-1503)AAA>TAA	p.K501*	MCF2L2_uc003flj.1_Nonsense_Mutation_p.K501*|MCF2L2_uc011bqr.1_Non-coding_Transcript	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	501					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(1)|breast(1)	4	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)											0.255474	92.868847	100.293359	35	102	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	183013262	183013262	9769	3	T	A	A	A	819	63	MCF2L2	5	3
LRRC15	131578	broad.mit.edu	37	3	194081543	194081543	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:194081543G>A	uc003ftt.2	-	c.248C>T	c.(247-249)TCA>TTA	p.S83L	LRRC15_uc003ftu.2_Missense_Mutation_p.S77L	NM_001135057	NP_001128529	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform a	77	Extracellular (Potential).					integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)										0.244755	77.732812	86.240422	35	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	194081543	194081543	9344	3	G	A	A	A	585	45	LRRC15	2	2
TGFBR2	7048	broad.mit.edu	37	3	30732969	30732969	+	Missense_Mutation	SNP	C	T	T	rs104893810		TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:30732969C>T	uc003cen.2	+	c.1657C>T	c.(1657-1659)CGT>TGT	p.R553C	TGFBR2_uc003ceo.2_Missense_Mutation_p.R528C	NM_001024847	NP_001020018	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II	528	Protein kinase.|Cytoplasmic (Potential).		R -> H (in LDS1B).|R -> C (in LDS1B).		activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis	caveola|external side of plasma membrane|transforming growth factor beta receptor complex	ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding			pancreas(9)|large_intestine(6)|stomach(3)|ovary(3)|lung(2)|central_nervous_system(1)	24										132				0.18543	60.90754	74.917706	28	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30732969	30732969	16350	3	C	T	T	T	299	23	TGFBR2	1	1
OSBPL10	114884	broad.mit.edu	37	3	31871586	31871586	+	Silent	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:31871586T>A	uc003cev.2	-	c.675A>T	c.(673-675)GCA>GCT	p.A225A	OSBPL10_uc003ceu.1_5'UTR|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	225					lipid transport		lipid binding				0				STAD - Stomach adenocarcinoma(1;0.00406)										0.12987	13.217973	23.468563	10	67	KEEP	---	---	---	---	capture		Silent	SNP	31871586	31871586	11686	3	T	A	A	A	704	55	OSBPL10	3	3
ITPR1	3708	broad.mit.edu	37	3	4748018	4748018	+	Missense_Mutation	SNP	A	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:4748018A>C	uc003bqa.2	+	c.4798A>C	c.(4798-4800)ATC>CTC	p.I1600L	ITPR1_uc010hca.1_Missense_Mutation_p.I1585L|ITPR1_uc011asu.1_Intron|ITPR1_uc003bqc.2_Missense_Mutation_p.I531L	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	1609	Cytoplasmic (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			ovary(4)|breast(2)|large_intestine(1)|kidney(1)|liver(1)|skin(1)|pancreas(1)	11				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)						2114				0.194444	19.207124	22.339607	7	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4748018	4748018	8224	3	A	C	C	C	208	16	ITPR1	4	4
WDR6	11180	broad.mit.edu	37	3	49050698	49050698	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49050698C>G	uc003cvj.2	+	c.1821C>G	c.(1819-1821)TGC>TGG	p.C607W	WDR6_uc011bbx.1_Intron|WDR6_uc011bby.1_Intron|WDR6_uc010hkn.2_Missense_Mutation_p.C551W|WDR6_uc011bbz.1_Missense_Mutation_p.C526W	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	577	WD 9.				cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)										0.21519	47.731677	53.645722	17	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49050698	49050698	17883	3	C	G	G	G	337	26	WDR6	3	3
DNAH1	25981	broad.mit.edu	37	3	52430796	52430796	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52430796G>A	uc011bef.1	+	c.11593G>A	c.(11593-11595)GAT>AAT	p.D3865N	DNAH1_uc003ddv.2_Missense_Mutation_p.D723N	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3930					ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.176471	95.433165	125.657019	54	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52430796	52430796	4779	3	G	A	A	A	585	45	DNAH1	2	2
FAM107A	11170	broad.mit.edu	37	3	58555486	58555486	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:58555486C>A	uc003dko.2	-	c.195G>T	c.(193-195)CTG>CTT	p.L65L	FAM107A_uc003dkm.2_Silent_p.L34L|FAM107A_uc003dkn.2_Silent_p.L34L|FAM107A_uc010hnm.2_Silent_p.L62L|FAM107A_uc003dkp.1_Silent_p.L34L	NM_007177	NP_009108	O95990	F107A_HUMAN	downregulated in renal cell carcinoma	34					regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)										0.147541	36.257912	58.195973	27	156	KEEP	---	---	---	---	capture		Silent	SNP	58555486	58555486	5586	3	C	A	A	A	314	25	FAM107A	2	2
GRM7	2917	broad.mit.edu	37	3	7348280	7348280	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:7348280A>G	uc003bql.2	+	c.974A>G	c.(973-975)CAG>CGG	p.Q325R	GRM7_uc011ata.1_Non-coding_Transcript|GRM7_uc011atb.1_Non-coding_Transcript|GRM7_uc010hcf.2_Non-coding_Transcript|GRM7_uc011atc.1_Non-coding_Transcript|GRM7_uc010hcg.2_Missense_Mutation_p.Q325R|GRM7_uc003bqm.2_Missense_Mutation_p.Q325R|GRM7_uc003bqn.1_5'UTR	NM_181874	NP_870989	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform b	325	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)	4					L-Glutamic Acid(DB00142)									0.163743	55.295276	73.661563	28	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7348280	7348280	7081	3	A	G	G	G	91	7	GRM7	4	4
CNTN3	5067	broad.mit.edu	37	3	74315674	74315674	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:74315674C>G	uc003dpm.1	-	c.2944G>C	c.(2944-2946)GAT>CAT	p.D982H		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	982	Fibronectin type-III 4.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)	4		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)										0.141809	110.751588	161.440239	58	351	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74315674	74315674	3780	3	C	G	G	G	390	30	CNTN3	3	3
EPHA6	285220	broad.mit.edu	37	3	96706286	96706286	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:96706286G>T	uc010how.1	+	c.563G>T	c.(562-564)CGT>CTT	p.R188L	EPHA6_uc003drp.1_Missense_Mutation_p.R188L	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	93	Ephrin-binding.|Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(3)|lung(3)|stomach(2)|breast(1)|skin(1)|ovary(1)|kidney(1)	12										480				0.230769	126.398842	140.209192	48	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96706286	96706286	5364	3	G	T	T	T	520	40	EPHA6	1	1
C4orf17	84103	broad.mit.edu	37	4	100451036	100451036	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:100451036C>A	uc003huw.2	+	c.467C>A	c.(466-468)TCT>TAT	p.S156Y	C4orf17_uc003hux.2_Non-coding_Transcript	NM_032149	NP_115525	Q53FE4	CD017_HUMAN	hypothetical protein LOC84103	156											0				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)										0.095652	2.129833	21.010314	11	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100451036	100451036	2347	4	C	A	A	A	416	32	C4orf17	2	2
CFI	3426	broad.mit.edu	37	4	110670479	110670479	+	Splice_Site_SNP	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:110670479T>A	uc011cft.1	-	c.1069_splice	c.e11-1	p.G357_splice	CFI_uc003hzq.2_Splice_Site_SNP_p.G146_splice|CFI_uc003hzr.3_Splice_Site_SNP_p.G349_splice|CFI_uc003hzs.3_Splice_Site_SNP_p.G342_splice	NM_000204	NP_000195			complement factor I preproprotein						complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)						317				0.153094	88.262207	123.574098	47	260	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	110670479	110670479	3422	4	T	A	A	A	715	55	CFI	5	3
ANK2	287	broad.mit.edu	37	4	114279402	114279402	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114279402A>G	uc003ibe.3	+	c.9628A>G	c.(9628-9630)ACT>GCT	p.T3210A	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Missense_Mutation_p.T512A|ANK2_uc011cgb.1_Missense_Mutation_p.T3225A	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3177					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.154412	39.631141	55.121132	21	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114279402	114279402	624	4	A	G	G	G	78	6	ANK2	4	4
TRAM1L1	133022	broad.mit.edu	37	4	118005823	118005823	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:118005823C>T	uc003ibv.3	-	c.727G>A	c.(727-729)GAT>AAT	p.D243N		NM_152402	NP_689615	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like	243	Cytoplasmic (Potential).|TLC.				protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane				central_nervous_system(1)	1														0.13913	21.128406	35.598624	16	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118005823	118005823	16996	4	C	T	T	T	377	29	TRAM1L1	2	2
SYNPO2	171024	broad.mit.edu	37	4	119952637	119952637	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:119952637C>T	uc010inb.2	+	c.2707C>T	c.(2707-2709)CCC>TCC	p.P903S	SYNPO2_uc010ina.2_Missense_Mutation_p.P903S|SYNPO2_uc003icm.3_Missense_Mutation_p.P903S|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Missense_Mutation_p.P831S	NM_133477	NP_597734	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform a	903						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2														0.078125	-2.454981	20.841057	10	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119952637	119952637	15978	4	C	T	T	T	390	30	SYNPO2	2	2
FAT4	79633	broad.mit.edu	37	4	126328260	126328260	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126328260G>T	uc003ifj.3	+	c.5533G>T	c.(5533-5535)GTG>TTG	p.V1845L	FAT4_uc011cgp.1_Missense_Mutation_p.V143L	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1845	Cadherin 18.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.153571	86.962149	119.07874	43	237	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126328260	126328260	5928	4	G	T	T	T	520	40	FAT4	1	1
PCDH10	57575	broad.mit.edu	37	4	134073054	134073054	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:134073054C>A	uc003iha.2	+	c.1759C>A	c.(1759-1761)CGT>AGT	p.R587S	PCDH10_uc003igz.2_Missense_Mutation_p.R587S	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	587	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1				LUSC - Lung squamous cell carcinoma(193;0.227)										0.09375	3.806907	19.732661	9	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134073054	134073054	11927	4	C	A	A	A	351	27	PCDH10	1	1
SPOCK3	50859	broad.mit.edu	37	4	167713350	167713350	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:167713350G>T	uc011cjq.1	-	c.716C>A	c.(715-717)ACA>AAA	p.T239K	SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjr.1_Missense_Mutation_p.T110K|SPOCK3_uc003iri.1_Missense_Mutation_p.T230K|SPOCK3_uc003irj.1_Missense_Mutation_p.T227K|SPOCK3_uc011cjs.1_Missense_Mutation_p.T179K|SPOCK3_uc011cjt.1_Missense_Mutation_p.T138K|SPOCK3_uc011cju.1_Missense_Mutation_p.T123K|SPOCK3_uc011cjv.1_Missense_Mutation_p.T132K|SPOCK3_uc003irk.3_Missense_Mutation_p.T227K	NM_001040159	NP_001035249	Q9BQ16	TICN3_HUMAN	testican 3 isoform 1	230					signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity	p.T227K(1)		large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)										0.189474	38.141864	46.78993	18	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167713350	167713350	15594	4	G	T	T	T	624	48	SPOCK3	2	2
GALNT7	51809	broad.mit.edu	37	4	174219404	174219404	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:174219404C>T	uc003isz.3	+	c.1104C>T	c.(1102-1104)ACC>ACT	p.T368T	GALNT7_uc011ckb.1_Intron	NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	368	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)										0.157895	16.035639	22.399378	9	48	KEEP	---	---	---	---	capture		Silent	SNP	174219404	174219404	6482	4	C	T	T	T	275	22	GALNT7	2	2
CLRN2	645104	broad.mit.edu	37	4	17524543	17524543	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:17524543C>A	uc003gpg.1	+	c.310C>A	c.(310-312)CTC>ATC	p.L104I		NM_001079827	NP_001073296	A0PK11	CLRN2_HUMAN	clarin 2	104	Helical; (Potential).					integral to membrane					0														0.134228	49.883477	88.58133	40	258	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17524543	17524543	3696	4	C	A	A	A	364	28	CLRN2	2	2
TBC1D1	23216	broad.mit.edu	37	4	38097635	38097636	+	Nonsense_Mutation	DNP	GG	TT	TT			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:38097635_38097636GG>TT	uc003gtb.2	+	c.2322_2323GG>TT	c.(2320-2325)TGGGAA>TGTTAA	p.774_775WE>C*	TBC1D1_uc011byd.1_Nonsense_Mutation_p.868_869WE>C*|TBC1D1_uc010ifd.2_Nonsense_Mutation_p.561_562WE>C*	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,	774_775						nucleus	Rab GTPase activator activity			ovary(1)	1														0.116667	30.113357	64.847002	28	212	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	38097635	38097636	16119	4	GG	TT	TT	TT	559	43	TBC1D1	5	2
UGDH	7358	broad.mit.edu	37	4	39511522	39511522	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:39511522T>C	uc003guk.1	-	c.669A>G	c.(667-669)GCA>GCG	p.A223A	UGDH_uc011byp.1_Silent_p.A126A|UGDH_uc003gul.1_Silent_p.A156A	NM_003359	NP_003350	O60701	UGDH_HUMAN	UDP-glucose dehydrogenase	223	Substrate binding.				glycosaminoglycan biosynthetic process|oxidation-reduction process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3					NADH(DB00157)									0.116279	8.992641	21.458855	10	76	KEEP	---	---	---	---	capture		Silent	SNP	39511522	39511522	17498	4	T	C	C	C	808	63	UGDH	4	4
SLAIN2	57606	broad.mit.edu	37	4	48381849	48381849	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:48381849C>G	uc003gya.3	+	c.846C>G	c.(844-846)GCC>GCG	p.A282A	SLAIN2_uc003gyb.1_5'Flank	NM_020846	NP_065897	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	282											0														0.117073	37.65847	67.213698	24	181	KEEP	---	---	---	---	capture		Silent	SNP	48381849	48381849	14861	4	C	G	G	G	275	22	SLAIN2	3	3
PDGFRA	5156	broad.mit.edu	37	4	55156695	55156695	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55156695G>T	uc003han.3	+	c.3096G>T	c.(3094-3096)GAG>GAT	p.E1032D	PDGFRA_uc003haa.2_Missense_Mutation_p.E792D	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	1032	Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.138462	31.606684	56.251804	27	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55156695	55156695	12082	4	G	T	T	T	451	35	PDGFRA	2	2
REST	5978	broad.mit.edu	37	4	57796165	57796165	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57796165G>C	uc003hch.2	+	c.1141G>C	c.(1141-1143)GAG>CAG	p.E381Q	REST_uc003hci.2_Missense_Mutation_p.E381Q|REST_uc010ihf.2_Missense_Mutation_p.E55Q	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	381	C2H2-type 7.				transcription, DNA-dependent	cytoplasm|nucleus	transcription repressor activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	Glioma(25;0.08)|all_neural(26;0.181)													0.155116	101.531567	135.961614	47	256	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57796165	57796165	13704	4	G	C	C	C	429	33	REST	3	3
POLR2B	5431	broad.mit.edu	37	4	57896476	57896476	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57896476G>T	uc003hcl.1	+	c.3346G>T	c.(3346-3348)GTT>TTT	p.V1116F	POLR2B_uc011cae.1_Missense_Mutation_p.V1109F|POLR2B_uc011caf.1_Missense_Mutation_p.V1041F|POLR2B_uc003hcm.1_Missense_Mutation_p.V609F	NM_000938	NP_000929	P30876	RPB2_HUMAN	DNA directed RNA polymerase II polypeptide B	1116					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)													0.140741	32.031981	48.850375	19	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57896476	57896476	12643	4	G	T	T	T	572	44	POLR2B	2	2
UGT2B7	7364	broad.mit.edu	37	4	69973836	69973836	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:69973836G>T	uc003heg.3	+	c.1106G>T	c.(1105-1107)AGA>ATA	p.R369I	UGT2B7_uc010ihq.2_Intron	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	369					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)	1														0.120623	30.224373	66.521622	31	226	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69973836	69973836	17520	4	G	T	T	T	429	33	UGT2B7	2	2
GC	2638	broad.mit.edu	37	4	72634043	72634043	+	Missense_Mutation	SNP	G	T	T	rs34941807		TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:72634043G>T	uc010iif.2	-	c.293C>A	c.(292-294)GCT>GAT	p.A98D	GC_uc003hgd.2_De_novo_Start_OutOfFrame|GC_uc010iie.2_Missense_Mutation_p.A79D|GC_uc003hge.2_Missense_Mutation_p.A79D	NM_000583	NP_000574	P02774	VTDB_HUMAN	vitamin D-binding protein precursor	79	Albumin 1.				hormone biosynthetic process|vitamin D metabolic process	cytosol|lysosomal lumen	actin binding|vitamin D binding|vitamin transporter activity			ovary(2)	2		all_hematologic(202;0.107)	Lung(101;0.148)		Cholecalciferol(DB00169)									0.107143	4.822167	13.387577	6	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72634043	72634043	6548	4	G	T	T	T	442	34	GC	2	2
FGF5	2250	broad.mit.edu	37	4	81207742	81207742	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:81207742C>G	uc003hmd.2	+	c.723C>G	c.(721-723)AGC>AGG	p.S241R	FGF5_uc003hme.2_3'UTR	NM_004464	NP_004455	P12034	FGF5_HUMAN	fibroblast growth factor 5 isoform 1 precursor	241					cell proliferation|cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell division|positive regulation of cell proliferation	extracellular space	fibroblast growth factor receptor binding|growth factor activity			ovary(1)	1														0.111111	24.130433	44.308409	15	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81207742	81207742	6092	4	C	G	G	G	337	26	FGF5	3	3
PRKG2	5593	broad.mit.edu	37	4	82096115	82096115	+	Splice_Site_SNP	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:82096115T>A	uc003hmh.2	-	c.462_splice	c.e2-1	p.S154_splice	PRKG2_uc011cch.1_Splice_Site_SNP_p.S154_splice	NM_006259	NP_006250			protein kinase, cGMP-dependent, type II						platelet activation|protein phosphorylation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7										728				0.147783	55.726934	79.897019	30	173	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	82096115	82096115	12966	4	T	A	A	A	715	55	PRKG2	5	3
SCD5	79966	broad.mit.edu	37	4	83626448	83626448	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:83626448G>A	uc003hna.2	-	c.351C>T	c.(349-351)TCC>TCT	p.S117S	SCD5_uc003hnb.3_Silent_p.S117S|SCD5_uc003hnc.2_Silent_p.S117S	NM_001037582	NP_001032671	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5 isoform a	117					fatty acid biosynthetic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)								68				0.081081	-0.119537	19.736435	9	102	KEEP	---	---	---	---	capture		Silent	SNP	83626448	83626448	14368	4	G	A	A	A	600	47	SCD5	2	2
MMRN1	22915	broad.mit.edu	37	4	90857222	90857222	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:90857222C>G	uc003hst.2	+	c.2391C>G	c.(2389-2391)AAC>AAG	p.N797K	MMRN1_uc010iku.2_Intron|MMRN1_uc011cds.1_Missense_Mutation_p.N539K	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	797					cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)										0.104762	15.543729	31.855523	11	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90857222	90857222	10061	4	C	G	G	G	259	20	MMRN1	3	3
GRID2	2895	broad.mit.edu	37	4	94159624	94159624	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:94159624G>T	uc011cdt.1	+	c.1228G>T	c.(1228-1230)GGC>TGC	p.G410C	GRID2_uc011cdu.1_Missense_Mutation_p.G315C|GRID2_uc010ikz.1_Missense_Mutation_p.G91C	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	410	Extracellular (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|large_intestine(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)									0.12093	26.486727	56.789218	26	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94159624	94159624	7050	4	G	T	T	T	611	47	GRID2	2	2
GRID2	2895	broad.mit.edu	37	4	94436452	94436452	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:94436452G>T	uc011cdt.1	+	c.2083G>T	c.(2083-2085)GGA>TGA	p.G695*	GRID2_uc011cdu.1_Nonsense_Mutation_p.G600*	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	695	Extracellular (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|large_intestine(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)									0.12	15.12841	32.846979	15	110	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	94436452	94436452	7050	4	G	T	T	T	455	35	GRID2	5	2
SMARCAD1	56916	broad.mit.edu	37	4	95197502	95197502	+	Silent	SNP	G	T	T	rs111425618		TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:95197502G>T	uc003htb.3	+	c.1821G>T	c.(1819-1821)GCG>GCT	p.A607A	SMARCAD1_uc003htc.3_Silent_p.A607A|SMARCAD1_uc003htd.3_Silent_p.A607A|SMARCAD1_uc010ila.2_Silent_p.A470A|SMARCAD1_uc011cdw.1_Silent_p.A177A	NM_001128430	NP_001121902	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated	607	Helicase ATP-binding.				chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)										0.169231	23.884121	30.615797	11	54	KEEP	---	---	---	---	capture		Silent	SNP	95197502	95197502	15270	4	G	T	T	T	470	37	SMARCAD1	1	1
UNC5C	8633	broad.mit.edu	37	4	96140295	96140295	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:96140295G>T	uc003htp.1	-	c.1470C>A	c.(1468-1470)CCC>CCA	p.P490P	UNC5C_uc010ilc.1_Silent_p.P509P|UNC5C_uc003htq.2_Silent_p.P509P	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor	490	Cytoplasmic (Potential).				apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)										0.177719	113.469461	150.380092	67	310	KEEP	---	---	---	---	capture		Silent	SNP	96140295	96140295	17551	4	G	T	T	T	548	43	UNC5C	2	2
SLC6A19	340024	broad.mit.edu	37	5	1213681	1213681	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:1213681C>A	uc003jbw.3	+	c.767C>A	c.(766-768)ACG>AAG	p.T256K		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	256	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)											0.235294	28.575786	31.844059	12	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1213681	1213681	15179	5	C	A	A	A	247	19	SLC6A19	1	1
SLC12A2	6558	broad.mit.edu	37	5	127516628	127516628	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127516628T>A	uc003kus.2	+	c.3154T>A	c.(3154-3156)TGT>AGT	p.C1052S	SLC12A2_uc010jdf.2_Non-coding_Transcript|SLC12A2_uc010jdg.2_Missense_Mutation_p.C1036S	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12	1052	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(2)	2		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)									0.293269	162.293469	170.251178	61	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127516628	127516628	14878	5	T	A	A	A	715	55	SLC12A2	3	3
FBN2	2201	broad.mit.edu	37	5	127727777	127727777	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127727777T>A	uc003kuu.2	-	c.1537A>T	c.(1537-1539)ACT>TCT	p.T513S	FBN2_uc003kuv.2_Missense_Mutation_p.T480S	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	513	EGF-like 6.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.306452	96.990452	101.141288	38	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127727777	127727777	5939	5	T	A	A	A	780	60	FBN2	3	3
ADAMTS19	171019	broad.mit.edu	37	5	128862065	128862065	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128862065G>C	uc003kvb.1	+	c.984G>C	c.(982-984)GAG>GAC	p.E328D	ADAMTS19_uc003kvc.1_Non-coding_Transcript	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	328	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)	8		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)						425				0.141791	40.131088	56.712156	19	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128862065	128862065	265	5	G	C	C	C	425	33	ADAMTS19	3	3
GFRA3	2676	broad.mit.edu	37	5	137593429	137593429	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137593429C>A	uc003lcn.2	-	c.684G>T	c.(682-684)GGG>GGT	p.G228G	GFRA3_uc003lco.2_Silent_p.G197G	NM_001496	NP_001487	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3 preproprotein	228					peripheral nervous system development	anchored to membrane|cytoplasm|extrinsic to membrane|intracellular membrane-bounded organelle	receptor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)											0.222222	19.748982	22.928351	10	35	KEEP	---	---	---	---	capture		Silent	SNP	137593429	137593429	6617	5	C	A	A	A	275	22	GFRA3	2	2
PCDHAC2	56134	broad.mit.edu	37	5	140346519	140346519	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140346519G>A	uc003lii.2	+	c.168G>A	c.(166-168)GCG>GCA	p.A56A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Silent_p.A56A	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	56	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			Melanoma(190;638 2083 3390 11909 52360)								0.333333	12.469279	12.838649	5	10	KEEP	---	---	---	---	capture		Silent	SNP	140346519	140346519	11953	5	G	A	A	A	483	38	PCDHAC2	1	1
PCDHB7	56129	broad.mit.edu	37	5	140554394	140554394	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140554394G>C	uc003lit.2	+	c.1978G>C	c.(1978-1980)GTG>CTG	p.V660L		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	660	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.094241	17.677825	49.202306	18	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140554394	140554394	11967	5	G	C	C	C	520	40	PCDHB7	3	3
PCDHB16	57717	broad.mit.edu	37	5	140562928	140562928	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140562928C>G	uc003liv.2	+	c.794C>G	c.(793-795)TCC>TGC	p.S265C	PCDHB16_uc010jfw.1_Intron	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	265	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.135294	40.841027	62.725457	23	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140562928	140562928	11961	5	C	G	G	G	390	30	PCDHB16	3	3
ANKH	56172	broad.mit.edu	37	5	14746065	14746065	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:14746065C>A	uc003jfm.3	-	c.829G>T	c.(829-831)GCG>TCG	p.A277S	ANKH_uc003jfl.3_5'UTR	NM_054027	NP_473368	Q9HCJ1	ANKH_HUMAN	progressive ankylosis protein	277	Cytoplasmic (Potential).				locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity				0														0.246575	39.808225	44.081259	18	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14746065	14746065	630	5	C	A	A	A	338	26	ANKH	2	2
DOCK2	1794	broad.mit.edu	37	5	169506137	169506137	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169506137C>A	uc003maf.2	+	c.5153C>A	c.(5152-5154)TCG>TAG	p.S1718*	DOCK2_uc011der.1_Non-coding_Transcript|DOCK2_uc010jjm.2_Nonsense_Mutation_p.S1210*|DOCK2_uc003mah.2_Nonsense_Mutation_p.S274*	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1718					actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.238806	37.866429	42.041526	16	51	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	169506137	169506137	4871	5	C	A	A	A	403	31	DOCK2	5	1
CDH10	1008	broad.mit.edu	37	5	24509715	24509715	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:24509715C>A	uc003jgr.1	-	c.1216G>T	c.(1216-1218)GTA>TTA	p.V406L	CDH10_uc011cnu.1_Non-coding_Transcript	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	406	Cadherin 4.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)										0.144737	38.141561	56.608442	22	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24509715	24509715	3225	5	C	A	A	A	221	17	CDH10	2	2
CDH6	1004	broad.mit.edu	37	5	31305452	31305452	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31305452C>A	uc003jhe.1	+	c.1171C>A	c.(1171-1173)CAA>AAA	p.Q391K	CDH6_uc003jhd.1_Missense_Mutation_p.Q391K	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	391	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|large_intestine(1)	5														0.280488	123.984365	131.085781	46	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31305452	31305452	3243	5	C	A	A	A	221	17	CDH6	2	2
CDH6	1004	broad.mit.edu	37	5	31322949	31322949	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31322949T>A	uc003jhe.1	+	c.1907T>A	c.(1906-1908)CTG>CAG	p.L636Q		NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	636	Helical; (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|large_intestine(1)	5														0.24186	123.688706	136.76485	52	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31322949	31322949	3243	5	T	A	A	A	715	55	CDH6	3	3
RNASEN	29102	broad.mit.edu	37	5	31526186	31526186	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31526186C>A	uc003jhg.2	-	c.854G>T	c.(853-855)AGA>ATA	p.R285I	RNASEN_uc003jhh.2_Missense_Mutation_p.R285I|RNASEN_uc003jhi.2_Missense_Mutation_p.R285I|RNASEN_uc010iui.1_Missense_Mutation_p.S276I	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	285	Arg-rich.				gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0														0.239437	73.271739	82.081045	34	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31526186	31526186	13894	5	C	A	A	A	312	24	RNASEN	2	2
IL7R	3575	broad.mit.edu	37	5	35876456	35876456	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35876456C>G	uc003jjs.2	+	c.1248C>G	c.(1246-1248)CCC>CCG	p.P416P	IL7R_uc011cop.1_Non-coding_Transcript	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	416	Cytoplasmic (Potential).				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)	4	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)											0.215385	68.195975	77.86775	28	102	KEEP	---	---	---	---	capture		Silent	SNP	35876456	35876456	8006	5	C	G	G	G	275	22	IL7R	3	3
ADCY2	108	broad.mit.edu	37	5	7698359	7698359	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:7698359G>T	uc003jdz.1	+	c.982_splice	c.e7-1	p.E328_splice	ADCY2_uc011cmo.1_Splice_Site_SNP_p.E148_splice	NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)	6														0.220859	150.900918	174.311212	72	254	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	7698359	7698359	295	5	G	T	T	T	455	35	ADCY2	5	2
PDSS2	57107	broad.mit.edu	37	6	107531724	107531724	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:107531724C>G	uc003prt.2	-	c.927G>C	c.(925-927)ATG>ATC	p.M309I	PDSS2_uc011eak.1_Missense_Mutation_p.M173I|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Missense_Mutation_p.M309I	NM_020381	NP_065114	Q86YH6	DLP1_HUMAN	prenyl diphosphate synthase, subunit 2	309					isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)										0.142857	37.020648	50.786861	16	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107531724	107531724	12115	6	C	G	G	G	377	29	PDSS2	3	3
AHI1	54806	broad.mit.edu	37	6	135611635	135611635	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:135611635C>T	uc003qgi.2	-	c.3514G>A	c.(3514-3516)GAG>AAG	p.E1172K	AHI1_uc003qgf.2_Non-coding_Transcript|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Missense_Mutation_p.E1172K|AHI1_uc003qgj.2_Missense_Mutation_p.E1172K	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a	1172						adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)										0.047354	-51.564419	26.952967	17	342	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135611635	135611635	416	6	C	T	T	T	377	29	AHI1	2	2
CCDC28A	25901	broad.mit.edu	37	6	139106400	139106400	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:139106400G>A	uc003qie.2	+	c.629G>A	c.(628-630)CGG>CAG	p.R210Q		NM_015439	NP_056254	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	210											0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)										0.159763	45.912008	64.554632	27	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139106400	139106400	2924	6	G	A	A	A	507	39	CCDC28A	1	1
FNDC1	84624	broad.mit.edu	37	6	159654335	159654335	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:159654335T>A	uc010kjv.2	+	c.2791T>A	c.(2791-2793)TCC>ACC	p.S931T	FNDC1_uc010kjw.1_Missense_Mutation_p.S816T	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	931						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)										0.150943	11.973458	18.155772	8	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159654335	159654335	6210	6	T	A	A	A	650	50	FNDC1	3	3
PDE10A	10846	broad.mit.edu	37	6	165827162	165827162	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165827162A>T	uc003quo.2	-	c.1105T>A	c.(1105-1107)TAC>AAC	p.Y369N	PDE10A_uc011egj.1_Non-coding_Transcript|PDE10A_uc011egk.1_Missense_Mutation_p.Y289N|PDE10A_uc003qun.2_Missense_Mutation_p.Y359N	NM_001130690	NP_001124162	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 1	359	GAF 2.				platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)	3		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	Esophageal Squamous(22;308 615 5753 12038 40624)								0.153846	13.669124	19.624996	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165827162	165827162	12051	6	A	T	T	T	182	14	PDE10A	3	3
TBP	6908	broad.mit.edu	37	6	170871052	170871052	+	Silent	SNP	G	A	A	rs112083427		TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:170871052G>A	uc003qxt.2	+	c.228G>A	c.(226-228)CAG>CAA	p.Q76Q	TBP_uc003qxu.2_Silent_p.Q76Q|TBP_uc011ehf.1_Silent_p.Q56Q|TBP_uc011ehg.1_Silent_p.Q76Q	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein	76	Poly-Gln.				cell death|general transcription from RNA polymerase II promoter|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	general RNA polymerase II transcription factor activity|promoter binding|repressing transcription factor binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)										0.75	8.726953	8.952731	3	1	KEEP	---	---	---	---	capture		Silent	SNP	170871052	170871052	16170	6	G	A	A	A	438	34	TBP	2	2
BTN2A1	11120	broad.mit.edu	37	6	26468562	26468562	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26468562G>A	uc003nib.1	+	c.1369G>A	c.(1369-1371)GAA>AAA	p.E457K	BTN2A1_uc003nic.1_3'UTR|BTN2A1_uc003nid.1_Missense_Mutation_p.E305K|BTN2A1_uc011dko.1_Missense_Mutation_p.E396K|BTN2A1_uc010jqk.1_Missense_Mutation_p.E217K	NM_007049	NP_008980	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1 isoform 1	457	Cytoplasmic (Potential).|B30.2/SPRY.				lipid metabolic process	integral to plasma membrane				ovary(1)	1														0.131429	25.896339	49.019205	23	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26468562	26468562	1594	6	G	A	A	A	585	45	BTN2A1	2	2
HIST1H3J	8356	broad.mit.edu	37	6	27858239	27858239	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:27858239C>G	uc003nka.2	-	c.332G>C	c.(331-333)TGT>TCT	p.C111S	HIST1H2BO_uc003nkc.1_5'Flank	NM_003535	NP_003526	P68431	H31_HUMAN	histone cluster 1, H3j	111					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1														0.107914	23.520288	44.706057	15	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27858239	27858239	7449	6	C	G	G	G	221	17	HIST1H3J	3	3
C6orf27	80737	broad.mit.edu	37	6	31740879	31740879	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31740879G>A	uc011dog.1	-	c.939C>T	c.(937-939)GCC>GCT	p.A313A	C6orf27_uc003nxd.2_5'UTR|C6orf27_uc011doh.1_Non-coding_Transcript	NM_025258	NP_079534	Q9Y334	G7C_HUMAN	G7c protein precursor	313						extracellular region				ovary(3)	3														0.190476	17.794654	21.541668	8	34	KEEP	---	---	---	---	capture		Silent	SNP	31740879	31740879	2467	6	G	A	A	A	444	35	C6orf27	2	2
NOTCH4	4855	broad.mit.edu	37	6	32184741	32184741	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32184741G>T	uc003obb.2	-	c.1842C>A	c.(1840-1842)CTC>CTA	p.L614L	NOTCH4_uc011dpu.1_Non-coding_Transcript|NOTCH4_uc011dpv.1_Non-coding_Transcript|NOTCH4_uc003obc.2_Silent_p.L614L	NM_004557	NP_004548	Q99466	NOTC4_HUMAN	notch4 preproprotein	614	EGF-like 15; calcium-binding (Potential).|Extracellular (Potential).				cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			ovary(5)|lung(5)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	14										693				0.163121	35.924587	51.145335	23	118	KEEP	---	---	---	---	capture		Silent	SNP	32184741	32184741	10954	6	G	T	T	T	418	33	NOTCH4	2	2
C6orf138	442213	broad.mit.edu	37	6	47976742	47976742	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:47976742G>A	uc011dwm.1	-	c.484C>T	c.(484-486)CTC>TTC	p.L162F	C6orf138_uc011dwn.1_5'UTR|C6orf138_uc003ozf.2_Missense_Mutation_p.L179F	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	179						integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1														0.16129	19.808784	26.578812	10	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47976742	47976742	2435	6	G	A	A	A	455	35	C6orf138	2	2
PKHD1	5314	broad.mit.edu	37	6	51768419	51768419	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:51768419G>C	uc003pah.1	-	c.6972C>G	c.(6970-6972)ATC>ATG	p.I2324M	PKHD1_uc010jzn.1_Missense_Mutation_p.I307M|PKHD1_uc003pai.2_Missense_Mutation_p.I2324M	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2324	PbH1 3.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.141463	61.229492	86.651798	29	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51768419	51768419	12396	6	G	C	C	C	421	33	PKHD1	3	3
FAM83B	222584	broad.mit.edu	37	6	54805781	54805781	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:54805781C>A	uc003pck.2	+	c.2012C>A	c.(2011-2013)TCA>TAA	p.S671*		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	671										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)													0.109091	9.212473	25.871356	12	98	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	54805781	54805781	5860	6	C	A	A	A	377	29	FAM83B	5	2
GFRAL	389400	broad.mit.edu	37	6	55223728	55223728	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55223728G>A	uc003pcm.1	+	c.744G>A	c.(742-744)GTG>GTA	p.V248V		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	248	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.10396	12.318963	43.866147	21	181	KEEP	---	---	---	---	capture		Silent	SNP	55223728	55223728	6619	6	G	A	A	A	574	45	GFRAL	2	2
F13A1	2162	broad.mit.edu	37	6	6224933	6224933	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:6224933C>A	uc003mwv.2	-	c.959G>T	c.(958-960)GGT>GTT	p.G320V	F13A1_uc011dib.1_Missense_Mutation_p.G257V	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	320					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)									0.114625	36.002891	73.026401	29	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6224933	6224933	5534	6	C	A	A	A	234	18	F13A1	2	2
BAI3	577	broad.mit.edu	37	6	69349249	69349249	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:69349249G>T	uc003pev.3	+	c.682G>T	c.(682-684)GGC>TGC	p.G228C	BAI3_uc010kak.2_Missense_Mutation_p.G228C	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	228	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(7)|skin(6)|pancreas(4)|central_nervous_system(3)|lung(3)|urinary_tract(1)	24		all_lung(197;0.212)								992				0.12	6.11856	16.759675	9	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69349249	69349249	1321	6	G	T	T	T	559	43	BAI3	2	2
SNRNP48	154007	broad.mit.edu	37	6	7594075	7594075	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:7594075G>T	uc003mxr.2	+	c.265G>T	c.(265-267)GAA>TAA	p.E89*	SNRNP48_uc003mxs.2_Non-coding_Transcript	NM_152551	NP_689764	Q6IEG0	SNR48_HUMAN	U11/U12 snRNP 48K	89					mRNA processing|RNA splicing	cytoplasm|U12-type spliceosomal complex	metal ion binding				0														0.186047	27.140398	35.095736	16	70	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	7594075	7594075	15357	6	G	T	T	T	429	33	SNRNP48	5	2
COG5	10466	broad.mit.edu	37	7	107013135	107013135	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107013135C>T	uc003vec.2	-	c.833G>A	c.(832-834)AGT>AAT	p.S278N	COG5_uc003ved.2_Missense_Mutation_p.S278N|COG5_uc003vee.2_Missense_Mutation_p.S278N	NM_006348	NP_006339	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform	278					intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)	2														0.12381	18.802161	33.332426	13	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107013135	107013135	3799	7	C	T	T	T	260	20	COG5	2	2
TMEM168	64418	broad.mit.edu	37	7	112424746	112424746	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:112424746C>A	uc003vgn.2	-	c.135G>T	c.(133-135)TTG>TTT	p.L45F	TMEM168_uc010lju.2_Missense_Mutation_p.L45F|TMEM168_uc011kmr.1_Intron	NM_022484	NP_071929	Q9H0V1	TM168_HUMAN	transmembrane protein 168	45	Helical; (Potential).					integral to membrane|transport vesicle				ovary(1)|central_nervous_system(1)	2														0.168539	25.363485	34.630885	15	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112424746	112424746	16617	7	C	A	A	A	272	21	TMEM168	2	2
FOXP2	93986	broad.mit.edu	37	7	114284743	114284743	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:114284743G>T	uc003vgz.2	+	c.1068G>T	c.(1066-1068)TCG>TCT	p.S356S	FOXP2_uc003vgu.2_Non-coding_Transcript|FOXP2_uc003vha.2_Silent_p.S239S|FOXP2_uc003vhb.2_Silent_p.S331S|FOXP2_uc011kmu.1_Silent_p.S348S|FOXP2_uc011kmv.1_Silent_p.S330S|FOXP2_uc010ljz.1_Silent_p.S239S|FOXP2_uc003vgx.2_Silent_p.S331S|FOXP2_uc003vhd.2_Silent_p.S331S|FOXP2_uc003vhc.2_Silent_p.S356S	NM_148898	NP_683696	O15409	FOXP2_HUMAN	forkhead box P2 isoform II	331					camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|lung(1)|breast(1)|pancreas(1)	7														0.120879	16.067988	28.882524	11	80	KEEP	---	---	---	---	capture		Silent	SNP	114284743	114284743	6273	7	G	T	T	T	509	40	FOXP2	1	1
PTPRZ1	5803	broad.mit.edu	37	7	121608168	121608168	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121608168T>C	uc003vjy.2	+	c.288T>C	c.(286-288)CAT>CAC	p.H96H	PTPRZ1_uc003vjz.2_Silent_p.H96H	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	96	Extracellular (Potential).|Alpha-carbonic anhydrase.				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9														0.128378	41.13219	61.032906	19	129	KEEP	---	---	---	---	capture		Silent	SNP	121608168	121608168	13272	7	T	C	C	C	634	49	PTPRZ1	4	4
TAS2R16	50833	broad.mit.edu	37	7	122634999	122634999	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:122634999G>A	uc003vkl.1	-	c.690C>T	c.(688-690)GCC>GCT	p.A230A		NM_016945	NP_058641	Q9NYV7	T2R16_HUMAN	taste receptor T2R16	230	Helical; Name=6; (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste	endoplasmic reticulum|external side of plasma membrane|integral to membrane|trans-Golgi network	bitter taste receptor activity|protein binding			ovary(1)	1														0.158228	43.776609	61.370794	25	133	KEEP	---	---	---	---	capture		Silent	SNP	122634999	122634999	16091	7	G	A	A	A	496	39	TAS2R16	1	1
POT1	25913	broad.mit.edu	37	7	124475408	124475408	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:124475408C>G	uc003vlm.2	-	c.1430G>C	c.(1429-1431)AGA>ACA	p.R477T	POT1_uc011koe.1_Non-coding_Transcript|POT1_uc003vlk.2_Non-coding_Transcript|POT1_uc003vll.2_Non-coding_Transcript|POT1_uc003vlo.2_Missense_Mutation_p.R346T|POT1_uc003vln.2_Non-coding_Transcript	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	477					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)								0.132653	53.306469	78.992776	26	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124475408	124475408	12689	7	C	G	G	G	416	32	POT1	3	3
PAX4	5078	broad.mit.edu	37	7	127253901	127253901	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:127253901A>T	uc010lld.1	-	c.447T>A	c.(445-447)AGT>AGA	p.S149R	PAX4_uc003vmf.2_Missense_Mutation_p.S147R|PAX4_uc003vmg.1_Missense_Mutation_p.S149R|PAX4_uc003vmh.2_Missense_Mutation_p.S147R	NM_006193	NP_006184	O43316	PAX4_HUMAN	paired box 4	157					cell differentiation|endocrine pancreas development|organ morphogenesis|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1						Ovarian(113;737 1605 7858 27720 34092)								0.140351	27.242364	41.460874	16	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127253901	127253901	11901	7	A	T	T	T	76	6	PAX4	3	3
ZC3HAV1	56829	broad.mit.edu	37	7	138745860	138745860	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:138745860G>T	uc003vun.2	-	c.2018C>A	c.(2017-2019)TCC>TAC	p.S673Y	ZC3HAV1_uc003vuo.2_Missense_Mutation_p.S134Y|ZC3HAV1_uc003vup.2_Missense_Mutation_p.S673Y	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1	673	WWE.				response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1														0.149123	48.686431	75.633421	34	194	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138745860	138745860	18163	7	G	T	T	T	533	41	ZC3HAV1	2	2
ZC3HAV1	56829	broad.mit.edu	37	7	138764850	138764850	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:138764850G>C	uc003vun.2	-	c.837C>G	c.(835-837)ATC>ATG	p.I279M	ZC3HAV1_uc003vuo.2_5'Flank|ZC3HAV1_uc003vup.2_Missense_Mutation_p.I279M	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1	279					response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1														0.059028	-16.677448	41.975329	17	271	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138764850	138764850	18163	7	G	C	C	C	577	45	ZC3HAV1	3	3
MGAM	8972	broad.mit.edu	37	7	141708386	141708386	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141708386G>A	uc003vwy.2	+	c.208G>A	c.(208-210)GCT>ACT	p.A70T		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	70	Ser/Thr-rich.|Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.12069	6.478606	14.668398	7	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141708386	141708386	9931	7	G	A	A	A	598	46	MGAM	2	2
OR6V1	346517	broad.mit.edu	37	7	142749605	142749605	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142749605C>G	uc011ksv.1	+	c.168C>G	c.(166-168)CCC>CCG	p.P56P		NM_001001667	NP_001001667	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V,	56	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.059)													0.14554	110.552114	162.042945	62	364	KEEP	---	---	---	---	capture		Silent	SNP	142749605	142749605	11622	7	C	G	G	G	262	21	OR6V1	3	3
CNTNAP2	26047	broad.mit.edu	37	7	146741088	146741088	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:146741088G>T	uc003weu.1	+	c.492G>T	c.(490-492)CTG>CTT	p.L164L		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	164	F5/8 type C.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)											0.09633	9.517166	45.131759	21	197	KEEP	---	---	---	---	capture		Silent	SNP	146741088	146741088	3785	7	G	T	T	T	600	47	CNTNAP2	2	2
CNTNAP2	26047	broad.mit.edu	37	7	146825920	146825920	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:146825920T>G	uc003weu.1	+	c.1075T>G	c.(1075-1077)TCA>GCA	p.S359A		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	359	Laminin G-like 1.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)											0.109589	32.840807	65.886526	24	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146825920	146825920	3785	7	T	G	G	G	702	54	CNTNAP2	4	4
KRBA1	84626	broad.mit.edu	37	7	149419947	149419947	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149419947G>T	uc003wfz.2	+	c.672G>T	c.(670-672)CGG>CGT	p.R224R	KRBA1_uc010lpj.2_Non-coding_Transcript|KRBA1_uc003wga.2_Non-coding_Transcript|KRBA1_uc003wgb.2_5'Flank	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	224										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)											0.180328	35.43699	47.062633	22	100	KEEP	---	---	---	---	capture		Silent	SNP	149419947	149419947	8754	7	G	T	T	T	535	42	KRBA1	2	2
DPP6	1804	broad.mit.edu	37	7	154684104	154684104	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:154684104T>A	uc003wlk.2	+	c.2512T>A	c.(2512-2514)TCC>ACC	p.S838T	DPP6_uc003wli.2_Missense_Mutation_p.S774T|DPP6_uc003wlm.2_Missense_Mutation_p.S776T|DPP6_uc011kvq.1_Missense_Mutation_p.S731T	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	838	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			NSCLC(125;1384 1783 2490 7422 34254)								0.097297	10.023228	40.067844	18	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154684104	154684104	4914	7	T	A	A	A	754	58	DPP6	3	3
HOXA5	3202	broad.mit.edu	37	7	27182747	27182747	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27182747C>T	uc003syn.1	-	c.480G>A	c.(478-480)GCG>GCA	p.A160A		NM_019102	NP_061975	P20719	HXA5_HUMAN	homeobox A5	160					negative regulation of angiogenesis|negative regulation of erythrocyte differentiation|positive regulation of apoptosis|positive regulation of myeloid cell differentiation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0						Colon(119;75 2200 7557 42868)								0.154589	47.390083	70.980728	32	175	KEEP	---	---	---	---	capture		Silent	SNP	27182747	27182747	7587	7	C	T	T	T	392	31	HOXA5	1	1
COBL	23242	broad.mit.edu	37	7	51096323	51096323	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:51096323C>T	uc003tps.2	-	c.2641G>A	c.(2641-2643)GAG>AAG	p.E881K	COBL_uc003tpr.3_Missense_Mutation_p.E824K|COBL_uc011kcl.1_Missense_Mutation_p.E824K|COBL_uc003tpp.3_Missense_Mutation_p.E610K|COBL_uc003tpq.3_Missense_Mutation_p.E765K|COBL_uc003tpo.3_Missense_Mutation_p.E366K	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	824										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.178218	32.681928	42.53507	18	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51096323	51096323	3791	7	C	T	T	T	377	29	COBL	2	2
ZNF479	90827	broad.mit.edu	37	7	57188289	57188289	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:57188289A>T	uc010kzo.2	-	c.833T>A	c.(832-834)TTT>TAT	p.F278Y		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	278	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3			GBM - Glioblastoma multiforme(1;9.18e-12)											0.164835	22.268352	31.976485	15	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57188289	57188289	18527	7	A	T	T	T	13	1	ZNF479	3	3
ZNF479	90827	broad.mit.edu	37	7	57188826	57188826	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:57188826G>T	uc010kzo.2	-	c.296C>A	c.(295-297)CCA>CAA	p.P99Q		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	99					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3			GBM - Glioblastoma multiforme(1;9.18e-12)											0.132075	25.053177	45.979361	21	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57188826	57188826	18527	7	G	T	T	T	611	47	ZNF479	2	2
ZFPM2	23414	broad.mit.edu	37	8	106814500	106814500	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:106814500G>C	uc003ymd.2	+	c.2190G>C	c.(2188-2190)CAG>CAC	p.Q730H	ZFPM2_uc011lhs.1_Missense_Mutation_p.Q461H	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	730					blood coagulation|transcription, DNA-dependent	nucleoplasm	DNA binding|RNA polymerase II transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)											0.146341	24.241511	34.103134	12	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106814500	106814500	18248	8	G	C	C	C	425	33	ZFPM2	3	3
NUDCD1	84955	broad.mit.edu	37	8	110334668	110334668	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110334668T>C	uc003ynb.3	-	c.143A>G	c.(142-144)GAT>GGT	p.D48G	NUDCD1_uc003yna.2_Missense_Mutation_p.D19G|NUDCD1_uc010mcl.2_5'UTR|NUDCD1_uc010mcm.1_5'UTR	NM_032869	NP_116258	Q96RS6	NUDC1_HUMAN	NudC domain containing 1 isoform 1	48										ovary(1)|breast(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)											0.082569	4.190652	23.517079	9	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110334668	110334668	11127	8	T	C	C	C	650	50	NUDCD1	4	4
PKHD1L1	93035	broad.mit.edu	37	8	110396316	110396316	+	Silent	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110396316C>T	uc003yne.2	+	c.435C>T	c.(433-435)ACC>ACT	p.T145T		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	145	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.086735	6.027262	39.918784	17	179	KEEP	---	---	---	---	capture		Silent	SNP	110396316	110396316	12397	8	C	T	T	T	275	22	PKHD1L1	2	2
PKHD1L1	93035	broad.mit.edu	37	8	110439382	110439382	+	Silent	SNP	A	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110439382A>G	uc003yne.2	+	c.2997A>G	c.(2995-2997)CTA>CTG	p.L999L		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	999	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.193548	47.511	55.649672	18	75	KEEP	---	---	---	---	capture		Silent	SNP	110439382	110439382	12397	8	A	G	G	G	171	14	PKHD1L1	4	4
PKHD1L1	93035	broad.mit.edu	37	8	110477365	110477365	+	Silent	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110477365G>T	uc003yne.2	+	c.8304G>T	c.(8302-8304)GGG>GGT	p.G2768G		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2768	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.102941	9.31241	41.288698	21	183	KEEP	---	---	---	---	capture		Silent	SNP	110477365	110477365	12397	8	G	T	T	T	548	43	PKHD1L1	2	2
CSMD3	114788	broad.mit.edu	37	8	113304844	113304844	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113304844C>G	uc003ynu.2	-	c.8710G>C	c.(8710-8712)GGG>CGG	p.G2904R	CSMD3_uc003yns.2_Missense_Mutation_p.G2106R|CSMD3_uc003ynt.2_Missense_Mutation_p.G2864R|CSMD3_uc011lhx.1_Missense_Mutation_p.G2735R	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2904	Extracellular (Potential).|Sushi 19.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.08365	10.531015	56.864418	22	241	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113304844	113304844	4087	8	C	G	G	G	273	21	CSMD3	3	3
CSMD3	114788	broad.mit.edu	37	8	113988108	113988108	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113988108G>T	uc003ynu.2	-	c.1300C>A	c.(1300-1302)CAG>AAG	p.Q434K	CSMD3_uc003ynt.2_Missense_Mutation_p.Q394K|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	434	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.115152	44.095695	92.264667	38	292	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113988108	113988108	4087	8	G	T	T	T	624	48	CSMD3	2	2
CSMD3	114788	broad.mit.edu	37	8	114111142	114111142	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:114111142T>A	uc003ynu.2	-	c.760A>T	c.(760-762)AGC>TGC	p.S254C	CSMD3_uc003ynt.2_Missense_Mutation_p.S214C|CSMD3_uc011lhx.1_Missense_Mutation_p.S254C|CSMD3_uc010mcx.1_Missense_Mutation_p.S254C	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	254	Extracellular (Potential).|CUB 2.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.100719	8.748142	30.87393	14	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114111142	114111142	4087	8	T	A	A	A	715	55	CSMD3	3	3
DERL1	79139	broad.mit.edu	37	8	124033690	124033690	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124033690C>A	uc003ypl.2	-	c.503G>T	c.(502-504)GGC>GTC	p.G168V	DERL1_uc003ypm.2_Missense_Mutation_p.G168V|DERL1_uc011lif.1_Missense_Mutation_p.G68V|DERL1_uc003ypn.2_Missense_Mutation_p.G168V	NM_024295	NP_077271	Q9BUN8	DERL1_HUMAN	Der1-like domain family, member 1 isoform a	168	Helical; Name=4; (Potential).				endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|intracellular transport of viral proteins in host cell|retrograde protein transport, ER to cytosol	integral to endoplasmic reticulum membrane	MHC class I protein binding|receptor activity				0	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)											0.113636	31.607607	70.445184	30	234	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124033690	124033690	4625	8	C	A	A	A	338	26	DERL1	2	2
LRRC6	23639	broad.mit.edu	37	8	133637568	133637568	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133637568C>A	uc003ytk.2	-	c.786G>T	c.(784-786)TTG>TTT	p.L262F	LRRC6_uc003ytl.2_Non-coding_Transcript	NM_012472	NP_036604	Q86X45	LRRC6_HUMAN	leucine rich repeat containing 6	262						cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)											0.1375	14.16401	24.346204	11	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133637568	133637568	9391	8	C	A	A	A	272	21	LRRC6	2	2
COL22A1	169044	broad.mit.edu	37	8	139628254	139628254	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139628254G>C	uc003yvd.2	-	c.3914C>G	c.(3913-3915)CCA>CGA	p.P1305R	COL22A1_uc011ljo.1_Missense_Mutation_p.P585R	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1305	Pro-rich.|Gly-rich.|Collagen-like 12.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.226027	90.797208	100.861781	33	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139628254	139628254	3819	8	G	C	C	C	611	47	COL22A1	3	3
KCNK9	51305	broad.mit.edu	37	8	140715079	140715079	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:140715079T>C	uc003yvf.1	-	c.157A>G	c.(157-159)AAC>GAC	p.N53D	KCNK9_uc003yvg.1_Missense_Mutation_p.N53D	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	53	Extracellular (Potential).					integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)											0.114286	9.658149	19.923658	8	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140715079	140715079	8377	8	T	C	C	C	819	63	KCNK9	4	4
PTK2	5747	broad.mit.edu	37	8	141712746	141712746	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:141712746G>A	uc003yvt.2	-	c.2356C>T	c.(2356-2358)CAG>TAG	p.Q786*	PTK2_uc011ljp.1_Nonsense_Mutation_p.Q72*|PTK2_uc003yvo.2_Nonsense_Mutation_p.Q392*|PTK2_uc011ljq.1_Nonsense_Mutation_p.Q459*|PTK2_uc003yvp.2_Nonsense_Mutation_p.Q432*|PTK2_uc003yvq.2_Nonsense_Mutation_p.Q290*|PTK2_uc003yvr.2_Nonsense_Mutation_p.Q704*|PTK2_uc003yvs.2_Intron|PTK2_uc003yvu.2_Nonsense_Mutation_p.Q764*|PTK2_uc003yvv.2_Nonsense_Mutation_p.Q664*|PTK2_uc011ljr.1_Nonsense_Mutation_p.Q764*	NM_005607	NP_005598	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform b	764	Interaction with TGFB1I1.				axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)							917				0.122093	21.446633	45.516358	21	151	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	141712746	141712746	13217	8	G	A	A	A	585	45	PTK2	5	2
DLGAP2	9228	broad.mit.edu	37	8	1497613	1497613	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:1497613C>A	uc003wpl.2	+	c.754C>A	c.(754-756)CAG>AAG	p.Q252K	DLGAP2_uc003wpm.2_Missense_Mutation_p.Q252K	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	331					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)										0.187919	56.307723	69.900924	28	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1497613	1497613	4740	8	C	A	A	A	325	25	DLGAP2	2	2
LPL	4023	broad.mit.edu	37	8	19818481	19818481	+	Silent	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:19818481C>G	uc003wzk.3	+	c.1209C>G	c.(1207-1209)CTC>CTG	p.L403L		NM_000237	NP_000228	P06858	LIPL_HUMAN	lipoprotein lipase precursor	403	PLAT.|Heparin-binding (By similarity).				chylomicron remodeling|fatty acid biosynthetic process|lipoprotein metabolic process|phospholipid metabolic process|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|positive regulation of sequestering of triglyceride|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	anchored to membrane|chylomicron|plasma membrane|very-low-density lipoprotein particle	heparin binding|lipoprotein lipase activity|phospholipase activity|receptor binding|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	Clofibrate(DB00636)|Gemfibrozil(DB01241)|Orlistat(DB01083)									0.153153	42.710391	55.475312	17	94	KEEP	---	---	---	---	capture		Silent	SNP	19818481	19818481	9294	8	C	G	G	G	366	29	LPL	3	3
PPP2R2A	5520	broad.mit.edu	37	8	26220330	26220330	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:26220330G>A	uc011laf.1	+	c.798G>A	c.(796-798)ATG>ATA	p.M266I	PPP2R2A_uc003xek.2_Missense_Mutation_p.M257I|PPP2R2A_uc003xeu.2_Missense_Mutation_p.M256I	NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein	256	WD 4.				protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)						58				0.109756	7.609548	19.977651	9	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26220330	26220330	12820	8	G	A	A	A	585	45	PPP2R2A	2	2
RAB11FIP1	80223	broad.mit.edu	37	8	37735071	37735071	+	Splice_Site_SNP	SNP	T	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:37735071T>G	uc003xkm.1	-	c.372_splice	c.e2-1	p.Q124_splice	RAB11FIP1_uc010lvz.1_Splice_Site_SNP|RAB11FIP1_uc003xkn.1_Splice_Site_SNP_p.Q124_splice|RAB11FIP1_uc003xkp.1_5'UTR	NM_001002814	NP_001002814			RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)	1		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)											0.155556	33.20575	43.389915	14	76	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	37735071	37735071	13352	8	T	G	G	G	715	55	RAB11FIP1	5	4
POTEA	340441	broad.mit.edu	37	8	43157198	43157198	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:43157198C>G	uc003xpz.1	+	c.778C>G	c.(778-780)CAA>GAA	p.Q260E	POTEA_uc003xqa.1_Intron	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	260										ovary(1)	1														0.100917	14.038675	31.366833	11	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43157198	43157198	12690	8	C	G	G	G	377	29	POTEA	3	3
RGS20	8601	broad.mit.edu	37	8	54859271	54859271	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:54859271C>A	uc003xrp.2	+	c.706C>A	c.(706-708)CAC>AAC	p.H236N	RGS20_uc003xrq.2_Missense_Mutation_p.H121N|RGS20_uc010lye.2_Missense_Mutation_p.H28N|RGS20_uc010lyf.2_Intron|RGS20_uc003xrs.2_Missense_Mutation_p.H89N|RGS20_uc003xrt.2_5'UTR	NM_170587	NP_733466	O76081	RGS20_HUMAN	regulator of G-protein signaling 20 isoform a	236					negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)											0.058824	-9.034138	11.761535	6	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54859271	54859271	13777	8	C	A	A	A	273	21	RGS20	2	2
RALYL	138046	broad.mit.edu	37	8	85774568	85774568	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:85774568C>G	uc003yct.3	+	c.490C>G	c.(490-492)CGT>GGT	p.R164G	RALYL_uc003ycq.3_Missense_Mutation_p.R151G|RALYL_uc003ycr.3_Missense_Mutation_p.R151G|RALYL_uc003ycs.3_Missense_Mutation_p.R151G|RALYL_uc010lzy.2_Missense_Mutation_p.R140G|RALYL_uc003ycu.3_Missense_Mutation_p.R78G|RALYL_uc003ycv.3_Missense_Mutation_p.R63G	NM_001100391	NP_001093861	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 1	151							identical protein binding|nucleotide binding|RNA binding			ovary(1)	1														0.234043	29.601883	32.643303	11	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85774568	85774568	13480	8	C	G	G	G	299	23	RALYL	3	3
MMP16	4325	broad.mit.edu	37	8	89053922	89053922	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:89053922C>A	uc003yeb.3	-	c.1591G>T	c.(1591-1593)GGC>TGC	p.G531C		NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	531	Hemopexin-like 4.|Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|kidney(1)|central_nervous_system(1)	5														0.203704	63.437784	76.6061	33	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89053922	89053922	10045	8	C	A	A	A	286	22	MMP16	2	2
MMP16	4325	broad.mit.edu	37	8	89131071	89131071	+	Silent	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:89131071T>A	uc003yeb.3	-	c.729A>T	c.(727-729)GTA>GTT	p.V243V	MMP16_uc003yec.2_Silent_p.V243V	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	243	Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|kidney(1)|central_nervous_system(1)	5														0.076923	-3.372207	15.680869	8	96	KEEP	---	---	---	---	capture		Silent	SNP	89131071	89131071	10045	8	T	A	A	A	678	53	MMP16	3	3
KIAA1429	25962	broad.mit.edu	37	8	95504896	95504896	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95504896T>C	uc003ygo.1	-	c.4792A>G	c.(4792-4794)ACC>GCC	p.T1598A	KIAA1429_uc010maz.1_Non-coding_Transcript	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	1598					mRNA processing|RNA splicing	nucleus				ovary(1)	1	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)											0.123404	53.343216	85.9122	29	206	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95504896	95504896	8540	8	T	C	C	C	754	58	KIAA1429	4	4
TP53INP1	94241	broad.mit.edu	37	8	95952305	95952305	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95952305G>C	uc003yhg.2	-	c.256C>G	c.(256-258)CAG>GAG	p.Q86E	C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron|TP53INP1_uc003yhh.2_Missense_Mutation_p.Q86E	NM_033285	NP_150601	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	86					apoptosis	PML body					0	Breast(36;8.75e-07)													0.091837	4.59508	21.046045	9	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95952305	95952305	16930	8	G	C	C	C	611	47	TP53INP1	3	3
GABBR2	9568	broad.mit.edu	37	9	101216375	101216375	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101216375G>T	uc004ays.2	-	c.1124C>A	c.(1123-1125)ACA>AAA	p.T375K		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor	375	Extracellular (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)									0.182927	28.553815	36.328723	15	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101216375	101216375	6407	9	G	T	T	T	624	48	GABBR2	2	2
SLC44A1	23446	broad.mit.edu	37	9	108123471	108123471	+	Splice_Site_SNP	SNP	G	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:108123471G>C	uc004bcn.2	+	c.761_splice	c.e8-1	p.G254_splice	SLC44A1_uc010mtk.1_Splice_Site_SNP_p.G254_splice|SLC44A1_uc004bco.1_Splice_Site_SNP_p.G46_splice	NM_080546	NP_536856			CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)									0.120567	22.867219	42.781679	17	124	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	108123471	108123471	15132	9	G	C	C	C	455	35	SLC44A1	5	3
OR1N1	138883	broad.mit.edu	37	9	125289132	125289132	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125289132C>A	uc004bmn.1	-	c.441G>T	c.(439-441)TGG>TGT	p.W147C		NM_012363	NP_036495	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1														0.136842	15.633072	27.747271	13	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125289132	125289132	11375	9	C	A	A	A	286	22	OR1N1	2	2
RALGPS1	9649	broad.mit.edu	37	9	129957388	129957388	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:129957388G>T	uc004bqo.1	+	c.929G>T	c.(928-930)GGT>GTT	p.G310V	RALGPS1_uc011mac.1_Missense_Mutation_p.G310V|RALGPS1_uc004bqq.3_Missense_Mutation_p.G310V	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1	310					small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1														0.146119	56.461486	82.740058	32	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129957388	129957388	13477	9	G	T	T	T	572	44	RALGPS1	2	2
ACER2	340485	broad.mit.edu	37	9	19424744	19424744	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19424744G>T	uc003zny.1	+	c.270G>T	c.(268-270)CAG>CAT	p.Q90H	ACER2_uc003znx.1_Non-coding_Transcript|ACER2_uc003znz.1_Missense_Mutation_p.Q41H	NM_001010887	NP_001010887	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	90	Helical; (Potential).				ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity				0														0.148515	43.803235	67.77056	30	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19424744	19424744	140	9	G	T	T	T	425	33	ACER2	2	2
TAF1L	138474	broad.mit.edu	37	9	32632534	32632534	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:32632534C>T	uc003zrg.1	-	c.3044G>A	c.(3043-3045)CGT>CAT	p.R1015H		NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1015					male meiosis|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding|transcription activator activity			lung(8)|large_intestine(3)|central_nervous_system(3)|skin(2)|ovary(2)|breast(1)|pancreas(1)	20			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)						234				0.177062	149.219132	198.056827	88	409	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32632534	32632534	16044	9	C	T	T	T	247	19	TAF1L	1	1
NOL6	65083	broad.mit.edu	37	9	33467207	33467207	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:33467207C>A	uc003zsz.2	-	c.1779G>T	c.(1777-1779)CAG>CAT	p.Q593H	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zsy.2_5'Flank|NOL6_uc003zta.2_Missense_Mutation_p.Q593H|NOL6_uc010mjv.2_Missense_Mutation_p.Q590H|NOL6_uc011lob.1_Missense_Mutation_p.Q541H|NOL6_uc003ztb.1_Missense_Mutation_p.Q593H	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	593					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)								OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.134021	14.501938	27.118192	13	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33467207	33467207	10928	9	C	A	A	A	311	24	NOL6	2	2
FAM75A5	727905	broad.mit.edu	37	9	65508135	65508135	+	Splice_Site_SNP	SNP	C	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:65508135C>T	uc004adx.3	-	c.247_splice	c.e2+1	p.A83_splice		NM_015667	NP_056482			hypothetical protein LOC26165							integral to membrane					0														0.086397	-0.855743	93.418476	47	497	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	65508135	65508135	5846	9	C	T	T	T	234	18	FAM75A5	5	2
PTPRD	5789	broad.mit.edu	37	9	8465591	8465591	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8465591C>A	uc003zkk.2	-	c.3589G>T	c.(3589-3591)GAT>TAT	p.D1197Y	PTPRD_uc003zkp.2_Missense_Mutation_p.D786Y|PTPRD_uc003zkq.2_Missense_Mutation_p.D786Y|PTPRD_uc003zkr.2_Missense_Mutation_p.D781Y|PTPRD_uc003zks.2_Missense_Mutation_p.D776Y|PTPRD_uc003zkl.2_Missense_Mutation_p.D1188Y|PTPRD_uc003zkm.2_Missense_Mutation_p.D1184Y|PTPRD_uc003zkn.2_Missense_Mutation_p.D786Y|PTPRD_uc003zko.2_Missense_Mutation_p.D783Y	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1197	Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.207101	70.11858	83.566992	35	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8465591	8465591	13256	9	C	A	A	A	377	29	PTPRD	2	2
C9orf64	84267	broad.mit.edu	37	9	86559772	86559772	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:86559772G>A	uc004anb.2	-	c.730C>T	c.(730-732)CAG>TAG	p.Q244*	C9orf64_uc004anc.2_Nonsense_Mutation_p.Q103*	NM_032307	NP_115683	Q5T6V5	CI064_HUMAN	hypothetical protein LOC84267	244											0														0.198529	54.336093	65.85315	27	109	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	86559772	86559772	2605	9	G	A	A	A	585	45	C9orf64	5	2
OMD	4958	broad.mit.edu	37	9	95179363	95179363	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:95179363G>T	uc004asd.3	-	c.478C>A	c.(478-480)CTT>ATT	p.L160I	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron	NM_005014	NP_005005	Q99983	OMD_HUMAN	osteomodulin precursor	160	LRR 3.				cell adhesion	proteinaceous extracellular matrix				ovary(2)	2										29				0.16	42.575887	61.857821	28	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95179363	95179363	11270	9	G	T	T	T	429	33	OMD	2	2
GPRASP2	114928	broad.mit.edu	37	X	101972152	101972152	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:101972152G>A	uc004ejk.2	+	c.2355G>A	c.(2353-2355)CAG>CAA	p.Q785Q	GPRASP2_uc004ejl.2_Silent_p.Q785Q|GPRASP2_uc004ejm.2_Silent_p.Q785Q|GPRASP2_uc011mrp.1_Silent_p.Q124Q	NM_138437	NP_612446	Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting	785						cytoplasm	protein binding			ovary(1)	1														0.166667	50.442194	66.885795	26	130	KEEP	---	---	---	---	capture		Silent	SNP	101972152	101972152	6999	23	G	A	A	A	425	33	GPRASP2	2	2
H2BFWT	158983	broad.mit.edu	37	X	103267765	103267765	+	Silent	SNP	G	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:103267765G>A	uc004elr.2	-	c.468C>T	c.(466-468)TCC>TCT	p.S156S		NM_001002916	NP_001002916	Q7Z2G1	H2BWT_HUMAN	H2B histone family, member W, testis-specific	156					nucleosome assembly	nuclear membrane|nucleosome	DNA binding			ovary(1)	1														0.379747	85.756667	86.749006	30	49	KEEP	---	---	---	---	capture		Silent	SNP	103267765	103267765	7214	23	G	A	A	A	496	39	H2BFWT	1	1
COL4A6	1288	broad.mit.edu	37	X	107418937	107418937	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107418937C>A	uc004enw.3	-	c.2780G>T	c.(2779-2781)GGA>GTA	p.G927V	COL4A6_uc004env.3_Missense_Mutation_p.G926V|COL4A6_uc011msn.1_Missense_Mutation_p.G926V|COL4A6_uc010npk.2_Missense_Mutation_p.G926V	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	927	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.242857	36.13325	40.359595	17	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107418937	107418937	3833	23	C	A	A	A	390	30	COL4A6	2	2
COL4A6	1288	broad.mit.edu	37	X	107447623	107447623	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107447623C>G	uc004enw.3	-	c.710G>C	c.(709-711)GGC>GCC	p.G237A	COL4A6_uc004env.3_Missense_Mutation_p.G236A|COL4A6_uc011msn.1_Missense_Mutation_p.G236A|COL4A6_uc010npk.2_Missense_Mutation_p.G236A	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	237	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.150943	16.529868	22.796335	8	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107447623	107447623	3833	23	C	G	G	G	338	26	COL4A6	3	3
AMOT	154796	broad.mit.edu	37	X	112024171	112024171	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:112024171T>A	uc004epr.2	-	c.2416A>T	c.(2416-2418)ACT>TCT	p.T806S	AMOT_uc004eps.2_Missense_Mutation_p.T397S|AMOT_uc011mtc.1_Missense_Mutation_p.T46S	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	806					actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1														0.31068	168.533411	175.105234	64	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112024171	112024171	585	23	T	A	A	A	754	58	AMOT	3	3
TFDP3	51270	broad.mit.edu	37	X	132351139	132351141	+	Missense	Complex_substitution	TNG	CNT	CNT			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:132351139T>C	uc004exb.1	-	c.1149A>G	c.(1147-1149)CCA>CCG	p.P383P		NM_016521	NP_057605	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	383					regulation of transcription, DNA-dependent	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.22807	67.202454	74.929119	26	88	KEEP	---	---	---	---	capture		Missense	Complex_substitution	132351139	132351141	16327	23	TNG	CNT	CNT	C	704	55	TFDP3	5	5
GPR112	139378	broad.mit.edu	37	X	135438316	135438316	+	Silent	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135438316C>A	uc004ezu.1	+	c.6919C>A	c.(6919-6921)CGA>AGA	p.R2307R	GPR112_uc010nsb.1_Silent_p.R2102R|GPR112_uc010nsc.1_Intron	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2307	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.267857	39.698705	42.424398	15	41	KEEP	---	---	---	---	capture		Silent	SNP	135438316	135438316	6903	23	C	A	A	A	399	31	GPR112	1	1
ATP11C	286410	broad.mit.edu	37	X	138825775	138825775	+	Silent	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:138825775T>C	uc004faz.2	-	c.2982A>G	c.(2980-2982)GGA>GGG	p.G994G	ATP11C_uc004fax.2_Silent_p.G202G|ATP11C_uc004fay.2_Non-coding_Transcript|ATP11C_uc004fba.2_Silent_p.G994G	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a	994	Extracellular (Potential).				ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)													0.4	28.898031	29.072342	8	12	KEEP	---	---	---	---	capture		Silent	SNP	138825775	138825775	1140	23	T	C	C	C	795	62	ATP11C	4	4
SPANXN3	139067	broad.mit.edu	37	X	142605176	142605176	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:142605176C>G	uc004fbw.2	-	c.44G>C	c.(43-45)AGC>ACC	p.S15T		NM_001009609	NP_001009609	Q5MJ09	SPXN3_HUMAN	SPANX-N3 protein	15										ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.26455	153.365667	162.839339	50	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142605176	142605176	15500	23	C	G	G	G	364	28	SPANXN3	3	3
PASD1	139135	broad.mit.edu	37	X	150840204	150840204	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150840204C>G	uc004fev.3	+	c.1390C>G	c.(1390-1392)CTC>GTC	p.L464V		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	464						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.295775	65.267864	67.904661	21	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150840204	150840204	11888	23	C	G	G	G	416	32	PASD1	3	3
PASD1	139135	broad.mit.edu	37	X	150841089	150841089	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150841089C>G	uc004fev.3	+	c.1872C>G	c.(1870-1872)TTC>TTG	p.F624L		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	624						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.300971	96.690417	100.331461	31	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150841089	150841089	11888	23	C	G	G	G	415	32	PASD1	3	3
FATE1	89885	broad.mit.edu	37	X	150889897	150889897	+	Nonsense_Mutation	SNP	A	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150889897A>T	uc004fex.2	+	c.265A>T	c.(265-267)AGA>TGA	p.R89*		NM_033085	NP_149076	Q969F0	FATE1_HUMAN	fetal and adult testis expressed transcript	89						endoplasmic reticulum|integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)													0.237624	51.045118	57.402588	24	77	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	150889897	150889897	5929	23	A	T	T	T	140	11	FATE1	5	3
IL9R	3581	broad.mit.edu	37	X	155234092	155234093	+	Missense_Mutation	DNP	GG	CT	CT			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:155234092_155234093GG>CT	uc004fnv.1	+	c.441_442GG>CT	c.(439-444)CTGGAC>CTCTAC	p.D148Y	IL9R_uc010nvn.2_Missense_Mutation_p.D127Y|IL9R_uc004fnu.1_Intron	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor	148	Extracellular (Potential).				cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.06383	-2.430752	16.174262	6	88	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	155234092	155234093	8009	23	GG	CT	CT	CT	600	47	IL9R	3	3
P2RY8	286530	broad.mit.edu	37	X	1584949	1584949	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:1584949T>C	uc004cpz.2	-	c.503A>G	c.(502-504)CAC>CGC	p.H168R		NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8	168	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.088235	1.610134	13.255953	6	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1584949	1584949	11768	23	T	C	C	C	767	59	P2RY8	4	4
DHRSX	207063	broad.mit.edu	37	X	2209645	2209645	+	Splice_Site_SNP	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:2209645C>A	uc004cqf.3	-	c.287_splice	c.e4-1	p.V96_splice		NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked						oxidation-reduction process		binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)												0.107843	17.186246	48.314033	22	182	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	2209645	2209645	4678	23	C	A	A	A	260	20	DHRSX	5	2
TMEM47	83604	broad.mit.edu	37	X	34648523	34648523	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34648523C>A	uc004ddh.2	-	c.453G>T	c.(451-453)TGG>TGT	p.W151C	TMEM47_uc010ngs.2_Non-coding_Transcript	NM_031442	NP_113630	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47	151						integral to membrane				lung(1)	1														0.146341	14.237311	24.115595	12	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34648523	34648523	16710	23	C	A	A	A	286	22	TMEM47	2	2
USP9X	8239	broad.mit.edu	37	X	41064746	41064746	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:41064746G>T	uc004dfb.2	+	c.5015G>T	c.(5014-5016)AGG>ATG	p.R1672M	USP9X_uc004dfc.2_Missense_Mutation_p.R1672M	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	1672					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			ovary(1)	1						Ovarian(172;1807 2695 35459 49286)								0.229167	46.392864	52.857223	22	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41064746	41064746	17654	23	G	T	T	T	455	35	USP9X	2	2
SSX3	10214	broad.mit.edu	37	X	48209509	48209509	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48209509G>T	uc004djd.1	-	c.379C>A	c.(379-381)CCA>ACA	p.P127T	SSX3_uc004dje.2_Missense_Mutation_p.P127T	NM_021014	NP_066294	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3 isoform a	127					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0						Colon(37;227 826 19399 40970 48007)								0.281879	207.583049	220.258424	84	214	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48209509	48209509	15723	23	G	T	T	T	546	42	SSX3	2	2
TSPY1	7258	broad.mit.edu	37	Y	9305908	9305908	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:9305908G>T	uc004frw.3	+	c.565_splice	c.e3-1	p.V189_splice	TSPY1_uc004frx.3_Splice_Site_SNP_p.V189_splice|TSPY1_uc010nwp.1_Intron	NM_003308	NP_003299			testis specific protein, Y-linked 1						cell differentiation|cell proliferation|gonadal mesoderm development|nucleosome assembly|spermatogenesis	cytoplasm|nucleus	identical protein binding				0														0.082222	-6.380449	73.566787	37	413	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	9305908	9305908	17208	24	G	T	T	T	455	35	TSPY1	5	2
INSRR	3645	broad.mit.edu	37	1	156815066	156815066	+	Frame_Shift_Del	DEL	C	-	-			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156815066_156815066delC	uc010pht.1	-	c.2239_2239delG	c.(2239-2241)GCAfs	p.A747fs	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	747	Extracellular (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(7)|ovary(4)|kidney(1)|central_nervous_system(1)|skin(1)	14	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)								p.A747T(H4-Tumor)	299				0.37			19	32		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	156815066	156815066	8075	1	C	-	-	-	338	26	INSRR	5	5
ANKRD36	375248	broad.mit.edu	37	2	97869978	97869978	+	Frame_Shift_Del	DEL	G	-	-			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:97869978_97869978delG	uc010yva.1	+	c.3039_3039delG	c.(3037-3039)AAGfs	p.K1013fs	ANKRD36_uc002sxp.3_Non-coding_Transcript	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1013											0														0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	97869978	97869978	673	2	G	-	-	-	451	35	ANKRD36	5	5
RPS4Y2	140032	broad.mit.edu	37	Y	22923177	22923179	+	In_Frame_Del	DEL	CAG	-	-			TCGA-44-2668-01	TCGA-44-2668-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:22923177_22923179delCAG	uc011nbb.1	+	c.270_272delCAG	c.(268-273)ATCAGC>ATC	p.S91del		NM_001039567	NP_001034656	Q8TD47	RS4Y2_HUMAN	ribosomal protein S4, Y-linked 2	91	S4 RNA-binding.				translation	ribosome	rRNA binding|structural constituent of ribosome				0														0.40			10	15		---	---	---	---	capture_indel		In_Frame_Del	DEL	22923177	22923179	14127	24	CAG	-	-	-	369	29	RPS4Y2	5	5
